I had this happen to me last week. I booked LAX-HNL-OGG-LAX on aa.com. The HNL-OGG leg was an HA codeshare.

I stayed overnight in HNL and was charged to check my bags from HNL-OGG. I was told by the HA gate agent that they don't waive the fee because they have their own loyalty program.

I contacted EXP desk and was told they don't have control over what HA charges. Said something about the fine print of "Other charges may apply".

Interestingly, if I hadn't stayed the night in HNL, HA would have handled my bags for no charge. The fact that I got my bags, stayed over night and then rechecked them caused the issue.

Fortunately only $20.