Please provide a step-by-step process of how the bug can be reproduced. The more details you provide us with the easier it will be for us to find and fix the bug:
Place foundation on plants which have been already on the ground
I’m not sure they implemented a sort of a plant decay, where plants would be removed when you place foundations on them. If they did this is definitely bugged.
Those plants have been there ever since you placed the foundation. You can’t harvest them and they never go. Next time, build a bit higher off the ground if you don’t want to see them.