Ok, did you do the same as the youtube video for on_crop_harvesting at time 15:00 in
I used to do animation work as a hobby, so I learned that doing a "," and "." in YouTube (comma for prior frame and period for next frame, but might be for Qwerty keyboard, so if that doesn't work, then check YouTube documentation for whatever keyboard you got) to go forward or backward in frames. YouTuber is doing a queue_free method in on_crop_harvesting, so it should delete your crop after it is done.
Or you can share your code and if I got time, I can try looking at it and see where the problem lies. I updated to Godot 4.5, but I kept my old Godot 4.4.1. So I am still able to edit the game, but I am not sure how longer I will keep 4.4.1 around.