I’m getting errors about hole clearance and solder mask bridging, and it’s reasonably obvious why - there is no aperture made in the zone for the through hole.
But why not? And why only for this particular piece of the zone (as far as I can tell). These two components are not even connected to anything in the schematic, so the two pads have different nets from each other, as well as from the zone.
I’ve never seen this happen before, and I’m stumped at the moment.
As is the way with these things, I made some progress shortly after posting, by moving some traces a bit, to ensure that the piece of the zone is not considered an island. I speculate that there is some internal inconsistency about exactly what constitutes an island, or exactly when this is determined, but I’ve never looked at the code base, so speculation is all it is.