Odd. I can't reproduce this bug. I've seen it happen once or twice though, but can't seem to make it happen on purpose. I'll play around with it more.
Maybe wait for 30 minutes before re-running the game.
So you plant a seed, do nothing for 30 minutes, exit the game and then run it again, and water it. Then see what happens. Takes a lot of time though, but I guess fixing every bug takes time xd
