For my penny's worth, I'm guessing from the way the OP has phrased it that there were three bags, but the laptop fitted in the suitcase so BA were in the OP's view wrong to charge.

However, if the first piece were full size and so too was the suitcase, then the OP has misunderstood the BA policy (and chosen one of the few flights where it will be enforced).

It is not two bags that fit in the sizer, it's one full size bag plus a smaller bag such as a laptop or handbag. BA actually have two different sizers for the two different types of bag.

If that analysis is correct and there was a large first bag, then if the laptop fitted in the suitcase I would be amazed if the suitcase were not over the limit for a second bag. In that case BA would rightly charge someone trying to take two full size bags on a basic fare.

Of course, the OP could return to say the laptop was in fact his only piece of hand luggage and describing it as the second piece was a mistake.