It sounds like both issues are likely caused by parts of the events being moved to the wrong places.
The seeds should work on their own without using any of the common events, because the player activates them by pressing the action button while standing on them. If they're holding seeds, those seeds will be planted on the event. If any part of spawning the seed event has been moved to a common event, it's going to plant them anywhere.
The same applies for anything using a <Self> variable. Because every crop event functions uniquely and independently, it can only be controlled through the <Self> variables. These also function by having the player press the action button while standing on the event, so no part of it should take place through the common event. The only thing you'll need to do in your common event is set the tool ID to the same ID as your watering can when the player presses the correct button. The rest should work as normal.
I hope that helps! :D