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I came across this sentence:

We thought that Joe didn’t go to the museum with the rest of the class.

The Manhattan Sentence Correction Guide says it’s an incorrect construction and it should be:

We thought that Joe hadn’t gone to the museum with the rest of the class.

What is wrong with the first one?

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    Where did you come across it? If it’s in a text book, I would suggest that you burn that book. Both sentences are perfectly fine and correct. Also, please use proper capitalisation when writing here—this is a site about advanced use of the English language, after all, and that includes proper orthography and punctuation. – Janus Bahs Jacquet Nov 12 '14 at 12:05
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    They're both correct. Which is preferable depends on context. – Peter Shor Nov 12 '14 at 12:05
  • Sorry for not capitalising, and i read that in Manhattan Sentence Correction Guide – Hari Krishna Nov 12 '14 at 12:08
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    This forum post actually has someone from the ManhattanGMAT staff try to justify that you can’t have “thought” in the same tense as a following “didn’t”, which is complete and utter nonsense. If the ManhattanGMAT project’s stance is that “We thought that he didn’t go” is incorrect, they are 100% wrong. – Janus Bahs Jacquet Nov 12 '14 at 12:14
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    Notice that all of the answerers are interpreting the first sentence to mean something far different from the second sentence. So, like many such questions, the answer depends on what you want to say. – Spencer Feb 17 '18 at 10:33
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Most grammar books try to explain the English tenses as if they were mathematical formulas - there's correct and there's not.

The problem is that the English tenses (and the English grammar, in general) are not mathematical formulas, and many times more than one tense fits the context.

there are cases where some specific tense is simply wrong for a specific context, like

I haven't seen her last week

we don't use the present perfect tense with a finished time period. not because it's "incorrect" but merely because it doesn't make any sense: the present perfect has many roles, discussing some action in some finished time period isn't one of them.

But this is a very specific case, and many times, it's not about "what's right" or "what fits here better" but it's more about "what do I want to emphasize"?

the Past Perfect emphasizes (among other usages) the fact that one action had finished (or hadn't finished) before another action in the past. the keyword here is emphasizes.

Don't look at me. the house had been a mess way before I got here.

in this case, I want to emphasize the fact the messiness of the house existed before I got there. I used the Past Perfect.

Usually, we can understand from the context what happened before what, and emphasizing the order of them is just redundant, or the order doesn't matter to begin with.

We thought that Joe didn’t go to the museum with the rest of the class.

Here, it's kind of obvious we though about Joe after he went (or didn't go) to the museum, and also, we don't care to much if our thinking happened before he went to the museum, it doesn't really matter here.

when more than one tense fits the context, think what you want to emphasize. when you hear a speaker speaks, think what he or she wants to emphasize by their tense choosing.

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The previous answer by @curiousdannii is right to note that both forms are acceptable here.

In fact "we thought that" can be considered a form of indirect or reported speech (a variant of 'they said that') and if you examine what the direct speech form would have been, you can make sense of this sentence:

It could have been

We thought, "Joe doesn't go to the museum"

When this is written as reported speech, it becomes

we thought that Joe didn't go to the museum

where 'doesn't' is converted into 'didn't' for the tense to be in agreement with the past tense form 'we thought.'

Now, what if the original sentence was

we thought, "Joe didn't go to the museum"

This is where the style guide might be putting the tense an extra degree into the past, from 'didn't' (simple past) to 'hadn't' (past perfect) as in

we thought that Joe hadn't gone to the museum.

However, it is not necessary, because 'didn't' already agrees with the past tense of 'we thought' and the strict rule of past perfect in terms of which event occured earlier is not relevant here, because this is a form of reported speech. So it is just as correct to write

we thought that Joe didn't go to the museum

or even

we had thought that Joe didn't go to the museum

although that sentence would need to be understood in its own time context depending on what comes before and what follows.

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Neither is incorrect, but the first one is markedly unusual, whereas the second one is very natural.

Both sentences are written in the past tense, but the second uses the perfect construction. The perfect changes what the reference point is. In this example it means that at the time when we were doing the thinking, our thoughts were about the past. If I was speaking in the present I could say

We think that Joe didn't go to the museum with the rest of the class.

To refer to this thought afterwards we shift both verbs. Think is in the present so we turn it on the past thought, but didn't go is already in the past, so we turn it into the past perfect hadn't gone.

The first sentence is more unusual. If we consider what its corresponding present tense version would be, we can see that it would be describing a habitual situation:

We think that Joe doesn’t go to the museum with the rest of the class.

This is a pretty weird non-habit to be commenting on, so although it is a grammatical possibility, it's unlikely to have been what was meant.

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    But this all depends on context, as @Peter Shor says. There is a time and place for 'I thought he didn't go', as there is for 'I thought he hadn't gone'. Let's say a teacher says to me 'Your son was an awful pain on the museum trip' I could say 'I thought he didn't go to the museum'. On the other hand if the teacher says 'the museum just called to say that a month ago your son knocked over an important exhibit when at the museum' I might say to my wife 'I thought he hadn't gone to the museum...' – WS2 Nov 12 '14 at 14:00
  • It may be a regional variety thing, but I'm not sure how natural it is in ny English to use 'didn't go' without the habitual meaning. – curiousdannii Nov 12 '14 at 14:15
  • I'm not sure what you mean by 'the habitual meaning', but certainly there are plenty of instances when I would use 'didn't go'. – WS2 Nov 12 '14 at 16:53
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    Just because the present tense is habitual, doesn't mean the past tense is habitual. Consider "I go to the gym today": weird, because you'd usually say "I'm going to the gym today". "I went to the gym yesterday": perfectly unobjectionable. So the correct present tense equivalent for the OP's sentence is: "We think that Joe isn't going to the museum with the rest of the class." – Peter Shor Nov 12 '14 at 22:04
  • @PeterShor that's a fair point. I wonder if this does vary in different dialects. For the record I speak Aus Eng. – curiousdannii Nov 13 '14 at 2:57
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What's wrong with the first one ("We thought that Joe didn’t go to the museum with the rest of the class") is that in most contexts, the going to the museum happened farther in the past than the thinking. In English, you indicate this by making sure that the more remote action is a more remote tense. "Had gone" is older than "thought."

It is possible to construct a context in which the sentence as written is the best fit. But most of the time the simple timeline approach that I outlined will stand you in good stead.

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    One can use the past perfect, but one doesn't have to. It is not required. In English, if you want to, you can use it to indicate specifically which event happened before which other. But mostly that's not necessary, and mostly we don't bother when it's obvious from the context, as here, what the sequence was. – John Lawler May 21 '18 at 2:43
  • @JohnLawler - I see your point. But I stand by my answer for two reasons. (a) When a student is confused about something in his textbook, he needs to be given some rationale for the author's point of view. I see this as a bit like when you send your child to play at your sister's house, with instructions to follow the house rules your sister has in place. It can be easier for the child to follow the "house rules" if some motivation for those rules is explained to the child. (b) I live with a non-native speaker of English. Things can get confusing quite quickly without the past perfect. – aparente001 May 21 '18 at 4:00
  • I agree with you that a native speaker can get away without it, but when a non-native speaker is making a variety of mistakes, it's often easier to intuit what they're really trying to say when they give you some extra hints. – aparente001 May 21 '18 at 4:01
  • When a student is confused about something in a textbook, they need to consider the possibility that the textbook is wrong. That's a very common feature of ESL textbooks; they can be and are written by anyone who believes they know something about English, they are full of gratuitously wrong grammatical "rules", and what they say is often believed as Gospel by students and teachers alike. If thy textbook offend thee, throw it out. – John Lawler May 21 '18 at 19:37
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    @JohnLawler - Of course. But I do think that it's helpful for English language learners (ELLs) to use the past perfect, even in situations where it's not required. Native speakers can get away with more ambiguity than ELLs. Liberal use of the past perfect can make communication more effective, which is especially helpful for ELLs. – aparente001 May 22 '18 at 4:54

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