Are you trying to water the trees through the trees' menus or through the watering can's menu in your inventory? I ask because the option on the watering can is always available, but trees only need/want water in intervals, not constantly.
I've been getting this a lot, too, lately but with stuff on the ground that I'm trying to pick up.
The last few times were with bags that I was trying to put back into my inventory - got to watching and noticed that, instead of just having "pick-up" and "rename", the verb "drop" was there on the bottom of the menu and it's what was causing the "verb not enabled" when trying to pick up the bags without paying attention when using the keyboard.