Hi @swwalsh1,
Thanks for the extra info. I would start by correcting the BIDS validation errors, at the very least errors 2, 4 and 5 are relevant for fmriprep.
It looks like you have two BOLD-correcting fieldmap pairs per session for this subject. Each BOLD image should only have one AP/PA pair associated with it. If you are putting all BOLDs into each IntendedFor that could explain the error. Additionally, the IntendedFor only needs to link to the BOLD, not sbref as well.
Best,
Steven