The only mod that adds new resources would be space exploration. It is noteworthy that the organizer was running fine without any errors until I updated to the newest factorio version. Perhaps something is related.
Strangely enough it also did not happen during new chunk discovery. I was well within active radar range, and all surrounding area has been mapped by my radars a long time ago.
Disabling the auto organization during generation made it stop, I don't know if I can reproduce it now.