Are they fruit flies? It's hard to tell from pics. If they're fruit flies you can set "traps" for them. We have a few in my house right now. You can just put a little bit of apple cider vinegar in a glass, open jar, etc. and add a drop of dish soap to break the surface tension. Some people also cover it with a piece of plastic wrap and poke holes in it, but I don't really see the point of that since they drown in the vinegar and can't get out anyway. If they are / could be fruit flies you could put one of those little traps near the enclosure so they're attracted to that instead of the water dish? Even if they're some other kind of bug that kind of trap might be worth a shot.
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