Amy: *Upon evading E-100:Zero after Final Egg* "PHEW! That was close! *Face slowly forms the most miserable and horrified expression possible before abruptly snapping back to stoic.*
When Gamma is transported to the past in a vision, it is unable to determine its location, and states "This presents a problem." It's the delivery of the line that makes it funny.
Similarly, Gamma demanding Amy that she "give him the bird." Of course, he means the bird she is carrying, but "the bird" is American slang for a very obscene gesture, which makes this scene look hilarious when looked in this context.
Everyone's faces in general when speaking. It seems Sonic Team wasn't too good at rigging.