The US DOT rule is that the allowance for the marketing carrier of the first segment applies to all segments of the same ticket. But, the DOT rule does not apply to waivers such as for status. Waivers, if there is one, are operating carrier dependent segment-by-segment.

In this case, the operating carrier of LHR-BCN was BA and thus BA's rules apply and OP does not get a bag waiver. He was properly charged. It may be that he was improperly not charged at BOS and OP is free to bring that BA's attention and send in some money. Or he could just leave it alone.

The delayed bag is an entirely separate issue and has nothing to do with the bag fee. The report should have been made to BA as the last delivering carrier (and it would almost certainly have taken no more than 10-15 minutes had OP done so), , but if IB took it, that is within IB's discretion. Presumably OP did not have any interim expenses for necessities during the 3 hours his bag was delayed, but if he did, those would be reimburseable by BA. He apparently had no such expenses, thus nothing to submit.

OP needs to put this behind him and be thankful that he was not charged a fee at BOS as well.