It looked like this, my first planting looked like that too but i still can harvest it.
This one gotta be a bug, i tried to take Arf with me when i got a full party slot and he just gone
Plants that are dark like that are rotten. You can still pick them up to free the farm plot, but you won't get anything from them.
Left row is rotten, right row is ready to harvest.
As for the Arf, yes, there was a check missing. Fixed it for the next version.
