Poppeteer is kinda broken, sometimes when you pluck someone you are not able to select the puppet and it makes it almost impossible to defeat the enemy. if you don't have a blimb bomb then it might as well be a gameover.
RPG Maker MV has a weird issue where if your cursor is hovering over something else that is selectable on screen you can't select something else. I've gotten a few reports for the same issue and it's typically that issue! If you move your cursor over to the Poppet it should be selectable