If you want, I can try taking a look at it. If you are on Windows 10 (I can no longer support Mac) send me your save files (you can find them at C:\Users\"account name"\AppData\LocalLow\OwenBellGames\Mendel). Describe exactly which plants your removing and I'll try and recreate it. It's a long time since I've touched the game code and I'm busy with other projects, so I can't guarantee I'll be able to fix it, but I'll at least see if I can find the bug.
Mendel Save Thanks for your time! The offending plants will be the "New Species" nearby when you load in.
Things I've tried: Moving the plants works, but even moving and deleting them will just have them reappear in their new position. Naming the species doesn't prevent it from reappearing, and I backed up this save and started a new island, the issue persists on the new island. I can confirm that I used to be able to delete plants, so if there's just been a hiccup along the way and a fresh install is the answer, well there are far worse things.
Thank you very much for your time and responses :)