Uh... I use "I'm confused" a lot. Because often I am confused! Someone said something that didn't make sense given what I know.

It divides fairly evenly (I think, being generous to myself here) between:

Yep, something I thought was true was not true.

Something they said was wrong, or they omitted something without which their meaning was ambiguous.

Maybe a smattering of "I/they misparsed what was said" too. But really. Often I'm just confused. When I use it I definitely don't mean they're an idiot I just worry that they'll think I'm an idiot... (...and that they might be right.)