Apologies for taking so long on following up on this! I've been testing the issue you reported with latest Prodigy version and it seems that after upgrading spacy-llm (currently at 0.7.1 in Prodigy 1.15.3) the issue is gone.
I know it's been a while so I won't be asking to confirm, but if you're still running into these issues after upgrading to latest Prodigy do ping us!
Thanks and, again, apologies for the late reply!