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sometimes Squirtle flutters his hands beside his ears.. like his hands are shaking. it doesn't happen very often which is why i find it a bit irregular. what does this mean?

The fluttering action is what turtles will do sometimes with another turtle as a territorial display or as part of a mating ritual. It's possible Squirtle is just fluttering at his reflection in the glass. When they get older, the male will flutter at a female to get her attention but sometimes they get confused and will flutter at a smooth round rock.

I have the same situation with my turtles too. Check out my forum titled TURTLE BEHAVIOR. You will be able to see what others have informed me of this type of behavior.