As the title suggests if my plants die in the garden, they go invisible. Not all plants do this, but it does do this often and it's very annoying as demonstrated in the screenshot below. Only way to get the plant to come back is for the gardener to come bring out Servo, but the gardener has an issue where she stops showing up altogether.
I had that same problem! Then all of a sudden, I was able to pick them up and delete them using the "move_objects on" cheat. Then I replaced them with more plants and it worked. I didn't have the problem again but since all these updates, I'm experiencing more issues that I never had before. So I haven't played the game in about a week. I just gave up completely. I wish they'd just fix it already.
this has been a bug since the games release but yes lots of issues keep propping up :(
