I think a lot of it has to do with where you're clicking. As you get used to the game, you figure out where you need to be clicking to get it to register correctly. This mainly happens in places with lots of overlapping textures (like a stove with a window above it with a curtain on it with a sink on one side and a microwave on the other). That being said, things are constantly improving and hopefully this will be one of those things.
Oh, and welcome to Project Zomboid! Glad to have you along.
