So you decided to make your own bug thread, but then post something that is not a bug?
If you point a gun at something and shoot, it'll die. That's how the airboat gun turret is coded.

The ragdoll in "Arena region" with the ammo box and mounted gun is not cleared when shooting the mop icon in the sky.

The button does say it doesn't always delete ragdolls.
For some reason the entire game does not recognize ragdolls as ragdolls.
The button uses "Ent_remove_all prop_ragdoll". A command that kills all ragdolls on the map.
But the game just does not realize that there's still ragdolls left.
Even if you aim at the ragdolls and enter "Ent_remove", it should delete the thing you look at, but the game just won't remove the ragdoll. because of some crap coding.

Antlion Worker acid goes through the target force field barrier. Not sure if you can do anything about it, just figured I'd put it in writing.

I have a mod installed that changed the combine shotgun soldier, but in the main area and npc range, it just showed the normal combine soldier holding the shotgun, not the modded shotgunner.

If both the npc and the "puppet" are the default combine, then your mod simply doesn't replace the second skin for the combine.
Because the map is set up to show the second skins when you spawn the npc a second time. I even double checked just to be sure i hadn't made a mistake.