If speaking or writing to someone and it becomes apparent they did not interpret something correctly, is it correct to inform them "you misunderstood" or "you misunderstand"? I'm not sure because the faulty assumption took place in the past but the person is still under the influence of the faulty assumption. On a related note, I was taught that when speaking of something that could happen it is spoken in the past tense but then why does it sound so unnatural to say something like "Since Bob is not a native English speaker he will surely misunderstood the meaning of the letter"?
I would choose You misunderstood because, as you say, this is an action that happened in the past: it happened when that person interpreted whatever. Besides, it sounds more polite to say You misunderstood (you made one mistake) than You misunderstand (you continue making the same mistake).
As for your second question, it does not sound unnatural: it is plain wrong. I don't know exactly what you were taught, but you cannot construct the future tense using the past tense. Of course, if it is something that could have happened, you would just write:
Since Bob is not a native English speaker, he surely misunderstood the meaning of the letter.
From the first two lines of your question, when someone doesn't interpret what you have said, "Misunderstood" is the correct term to be used, because things have already happened. Since it is a faulty assumption which already took place, we have to use the past tense.
You could use, You dont Understand! when the communication is happening at present.
Since Bob is not a native English speaker he will surely misunderstood the meaning of the letter, is very wrong.
It must be either,
Since Bob is not a native English speaker he will misunderstand the meaning - if it is going to happen in future
Since Bob is not a native English speaker he has misunderstood the meaning - if it has already happened
It depends on the other words surrounding the misunderstand / misunderstood.
The simple answer to your question: 'You misunderstood' is correct. 'You misunderstand' must have other words before or after the phrase to be correct in your situation (as you indicated that it happened in the past).
For example, if you added 'Did' before your second suggestion of 'you misunderstand' ("Did you misunderstand the question?"), it would be accurate. In this context, 'did' is a past tense auxiliary verb connected with a root verb. See (http://www.gingersoftware.com/grammarbook/verbs/do-does-did/ under the section 'The verb to do as an auxiliary verb'. In your situation (a situation that already occurred), without the addition of 'Did', it would not be correct.
If you don't add anything else to the sentence (regarding a situation that occurred in the past), I would use 'You misunderstood'. It is a simple past tense verb. (See http://en.bab.la/conjugation/english/misunderstand under Simple Past Tense).
For the second question, as others have said, it is not correct. You are using a future tense auxiliary verb (will) combined with a past tense verb (misunderstood). Instead, it should be a future tense auxiliary (helper) verb combined with the root verb (it is the same concept as the first link above).
I hope this helps.