At this point, I think I might try another file from scratch, not an ideal scenario but I don’t see a way to solve the problem and Nintendo ain’t gonna fix it anytime soon.
Even with the seeds caught, it doesn’t spawn any longer, starting to think it may be a bug from the NSO emulation since there are no other reports from this happening in the internet and the post is recent, so I’m supposing OP is also playing on the switch.