It depends.

If you can remove what they are too close to they will change back to green.

Sometimes I have had ones that were on top of an area I removed a large rock but I think rock bits were left behind under the soil and things wouldn't grow there. They will just vanish once the growing cycle ends though.

Not sure how the game handles a bunch of crops too close to each other though. If they are all bad perhaps selective culling by punching them would help.. but if the game just allows every other one or something then I would probably just leave it and learn to make them a bit further apart.