It was just that.

[aachu]

I have seen people say, for example, "It's not that we are being unhelpful, It's just that we don't understand your question". What does "it's just that" mean?

[Hedwig]

You could paraphrase it as 'it's only that' or 'it's simply that' we don't understand your question.

Does this help?

(Not a teacher)

[allenman]

What does "it's just that" mean?

You could say "the fact is" for this example.

Not a teacher - AmE native

[Tdol]

To me, it also has an underlying meaning that they are trying to avoid conflict and anger by giving you this reason.