Had something similar happen at YYZ customs, AC did not transfer my bag with wine in it to UA and it ended up with CBSA (who were surprisingly nice unlike my experiences with US CBP).

A call to CBSA straightened things out and the bag was re-released to AC who this time transferred it correctly to UA where it went through US CBP, then stateside and eventually home.

That was a few years ago, hopefully the info is still relevant.