So today I was making my 24 large plot with Couch Potatoes. I realized that i couldn't delete my wooden crates (To plant my King Parsley because that is a like). I logged out and back in and I couldn't get rid of them. I collected everything in the house but it still didn't work.
You need to either dig up the plant that is on top of the crates, or just wait until it's elder harvest to move them. Never plant the seed in air gardens with crates in place, I learned that the hard way too.