I planted some Knobbly Tree Nuts and their first stage looked like their third stage for some reason. They grew normally into the 2nd and then the 3rd stage (via Tree Jam), so it was just a visual bug.
Eventually, I applied Tree Jam on the fully grown Knobbly Tree for the second time and exited the game.
I rejoined later and I saw this:
Also, sometimes, this happens instead:
Not sure, I suppose relogging might be one cause of the bug, but that doesn't explain the wrong initial stage.