I think it's not a matter if it was a penalty or not, it was a matter of Champions League standards. Even if it was a 50/50 penalty, it should've never been called in such an important match, more so that it was in the last minute of the extra time. These very soft penalties are mostly called on friendly matches and unimportant league matches.
However, this is not the first time that Real Madrid cheated their way to the next rounds of CL, it has happened before (vs. Bayern, vs. Atletico, vs. Manchester etc.) and it will definitely happen again as long as Uncle Perez is on charge. They are simply purchasing the Champions League trophies, while they're jack ish otherwise.