Quote Originally Posted by SomethingBig
Aeris looking at Cloud strangely at the end could be due to Cloud's change of clothing, which, in turn, would trigger Cloud's look of embarrassment. That, or Cloud was embarrassed that he got separated from everyone else.
I'm pretty certain that in FFVII, Aeris always used to look at Cloud like that. She does it so that she can mantain eye contact with him whenever he looks at the floor.

So it's nothing to do with changes of clothing, really.