There is a pragmatic use of "just" in utterances such as "It's just that" as a discourse marker to deflect a counterargument. It's used in the same way as what is explained in the summary of the article below about entitled "I'm just saying" [that]. This usage should be analyzed as pragmatics or discourse analysis. The grammar of this form is dictated by the speaker's strategy but the clause precedes an argument that will be presented after it in another clause or refer back to it.
It can take the forms such as: "It's just that", [etc.] or it can be associated with a verb, "She just thinks that" or "I'm just saying that".
1 - It's just that they won.
just that [rest of clause] means there has been a discussion of some kind previously:
Imagine a conversation where someone says, about a football team:
A: They did not play really well last night at all, you know.
B: I know that but it's just that they won and I wish they hadn't.
Here the fact they won is what is bothering speaker B.
Imagine another conversation:
A: You've been complaining for ages about your sales' team. I don't get it.
B: It's just that they don't do what they are supposed to do. And I'm tired of it.
Here the fact they are doing what they are supposed to do is bothering speaker B.
Just that in speech such as that is used to make a specific point that is important to a speaker. In that sense, it is a deictic discourse marker in reference to other things that have been said.
2 - She just thinks they won.
- Someone else thinks otherwise. Here, it is similar to the case above. And can be used like that. It can mean that her main preoccupation is that they won and someone else thinks they did not, for example.
But it can also mean (depending on context): She only thinks that, and has no other particular thoughts about the situation. Then, it's a straight adverb.
3 - She thinks just that they won=is not grammatical (as either regular grammar or the grammar of spoken English). Though a speaker might pause and say something like: She thinks......just that they won, as a way of trying to say after it is too late to say it the other way: She just thinks that they won.
Article: ‘I’m Just Saying . . .’: Discourse Markers of
ROBERT T. CRAIG and ALENA L. SANUSI, University of Colorado.
Our central claim is that these 'saying' expressions are pragmatic devices by which speakers claim 'all along' to have held a consistent argumentative standpoint, one that continues through the discussion unless changed for good reasons. Through close analysis of a series of discourse examples, we show how these discourse markers are used to display continuity, deflect counterarguments, and acknowledge the force of counterarguments while preserving continuity.
[Unfortunately, the article is behind a paywall].