@User thanks for looking at that. I tried your suggestion but still hit the same issue.
At this juncture I need to focus on other things so I'm just going to insert bipolars right at the end and do LVS without them. I also have a resistor issue so same plan there. I'm fairly certain they're correct by inspection so just going to carry the risk.
I've created GitHub issues for both items to maintain traceability and can loop back to track down solutions when there's more breathing space.