If it doesn't feel right to you, the reasons don't matter. If you find somewhere else that you like better, and feels better, then switch. The feeling of leaving your boys somewhere you're not comfortable can't be nice.

As for those specific issues, the last one is just an accident. I'd be upset, but as long as there's an apology I'd be ok, I've done things like that myself and I'm sure the staff member feels bad. The first one, they know when you're getting there. They open 15 minutes before that, there should be someone ready and waiting for them. I'd bring it up with them because you don't need to be wasting time waiting or looking for someone.

The second one would annoy me the most. I know they have their own routines, but at that age I'm guessing there's an adjoining room with cots, so it's not like it's a group nap in the main room and it would mess things up for them, surely they can put them down 2 hours earlier, when you ask them to!

If those issues can't be resolved, and you're not liking it, I'd move them.