Also remember that it was quite dark in the well. Telling dog bones and human child bones apart in a dark well while you're under stress isn't an easy thing to do.
As far as Mycroft's and Sherlock's relationship is concerned, I think "resentment" is a far too strong a word to discribe Sherlock's feelings towards his brother. I think it's obvious in TEH that he actually quite enjoys his brother's company, even if he'd never openly admit it. And he wants him to be there at John's wedding for support. He values his opinion and we see in his mindpalace scenes, for example in TSoT, that he feels like Mycroft is the one pushing him to be as good as he can. I think a lot of Sherlock's sometimes seemingly resentful behaviour against his brother comes from Mycroft constantly lecturing him that caring and emotions are a weakness (because he wants to protect Sherlock from experiencing more pain). Sherlock wants his elder brother's respect and therefore makes sure he doesn't show any brotherly love or compasstion that could make him seem weak. I think their relationship makes sense: Mycroft being the elder one, always feeling the need to protect his seven years younger brother from the pain he had to endure in the past and from future pain and at the same time pushing him to become the most intelligent person he can be. Because I think that was what he was doing by telling Sherlock that he - Mycroft - was the clever one: Pushing Sherlock to challange him, to become better and to give his best. Probably Sherlock sometimes mistook Mycroft's actions for bullying and reacted accordingly, but I think subconsciously he knows that Mycroft's intentions were/are good, why else would he have such a prominent position in his mindpalace, pushing him to get to the right conclusion. He just doesn't want his brother to see him weak, that's why he pushes him away whenever he's in a vulnarable position.
Ok, that became way longer than I had intended, sorry. As far as Sherlock saying that he wasn't the one upsetting Mummy in aSiP, we can only guess. Maybe the parents and Mycroft sometimes went to visit Eurus before she was brought to Sherrinford. It would be only logical that Mummy would usually be quite upset when they came home from those visits and Sherlock would just assume that Mycroft had done something to upset her. Or probably Mycroft even took the blame willingly, he seems to have a habit of doing so.