Skimming the code it seems that the Mycelium Plant Growth State was added for Mushrooms. When you move from Planted to this stage (which is second in line), there is a check if the plant is a mushroom and if not it just skips over this stage. However, this check is only enabled for EP7, so if you don't have Supernatural it will simply assign the Mycelium Growth State after the Planted one.
I'm not entirely sure if/how this causes the actions to be thrown out of queue, but this explains the wrong Mycelium state of plants and since it's a combination that shouldn't happen (Mycelium on a non-mushroom), it might cause follow-up errors. I'll see if I can actually reproduce the kicking out of queue and if it only happens if there is a Mycelium state plant (for me, I could harvest two in a row in my garden where I had manually moved from the Mycelium state to the next).