There were grammarians in antiquity, and they analyzed Latin. Several grammarians have studied various aspects of Latin grammar in the modern era as well. I find it hard to believe that modern scholars would be in perfect agreement with the ancient ones. Is there something about Latin grammar that we confidently think we understand now but one or more Roman grammarians misunderstood? If there were several such misunderstandings or discrepancies, what were the biggest or most important ones? The Romans did not have the theoretical framework we have today and were bound to misunderstand something; it is unlikely in any field that modern theorists agree perfectly with ancient ones. Let me exclude etymology from this question and restrict it to other aspects of the language.