Maybe you were in the tutorial level, in this one the flies behavior is blocked in order to help you to familiarising yourself with the weapons.
Here's some commentary from a second playthrough: I chose the campsite instead and was pleased to see the flies swarming me, nullifying my earlier concerns to an extent. (I still think even in the tutorial they should buzz around, but that's besides the point)
Variety in weapons allowed for some style in the bug swattin', and I like the big boys that required a little extra bonkin'. Since they're flying, perhaps you could vary/randomize their height, and as they approach, they descend? More lightning bolts would be fun, too!