After you shake or hit each tree with your net, then Save & Continue. That will reset all the bugs & fish and you can do it all over again. I do this when I'm trying to get a "rock" bug to come out. Hit all the rocks, no bugs come out. Save & Continue and then hit all the rocks again. May take me several Save & Contiues, but at some point a bug will come out from under a rock. Should work the same way with tree bugs.
Good Luck.
