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"it is just that" is usually used as a polite way to disagree with what other says, or to politely say no to a request.

Is it idiomatic that one uses it for adding an extra point to what one just mentioned.

Example:

Group A require intentionality for moral act, group B don't. So the act described here is moral according to both A's and B's view. It is just that "intentional moral act" is not a proper term in the view of group A, because in their view there is no such thing as "unintentional moral act".

Is "it is just that" used idiomatically in the above sentence. If not, what to use instead?

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It's entirely idiomatic, and will help you sound more like a native speaker. Note that you're better off using the contracted form:

It's just that ...

Also note that it does not have to introduce a disagreement. The idiom can make a positive assertion.

I don't know why I'm humming tunes today. It's just that I feel so good.

  • But I would not use it in a report, or essay. It's really more appropriate to spoken English. In that context, I would use "but" or "however" (or, if it was not opposing what came before, "indeed" or "furthermore".). – Colin Fine Dec 17 '17 at 21:26
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It was s just that :

You use the expression it's just that when you are making a complaint, suggestion, or excuse, so that the person you are talking to will not get annoyed with you.

  • I'm sorry I struck you. I didn't mean to. It's just that I was so mad. Your hair is all right; it's just that you need a haircut.

(Collins Dictionary)

It is used also to suggest something, as in the sentence you are asking about.

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