The first is that most historians are not dispassionate observers concerned with recording literal truths; they are concerned with narratives containing moral truths. And, especially historically, lying about the facts to arrive at the moral truths was not beneath them. The history of Sparta is a classic example: our Greek sources here all talk up how wonderful Sparta is with its notions of equality and avoidance of luxury, and contain postscripts saying "but of course, this is the Sparta of yesteryear and not the Sparta of today, which is exactly the kind of wastrel that I'm condemning." I do want to be clear that this kind of moralism-over-literal-truth does happen all the time today, and it's definitely visibly strong in the textbook version of history taught today. Consider how US history courses at the grade school level tend to present the US as a moralizing force of liberty and democracy and manage to completely omit traumatic events such as King Philip's War, the deadliest war ever fought on (then-future) US soil, perhaps partly because it is rather inconvenient for the narrative of pious Pilgrims peacefully coexisting with Native Americans.
Specific to the Middle Ages, though, the humanism and Enlightenment movement that happens after that time did try quite hard to discredit any idea of progress in that time period and draw push their modernism as a rebirth of the glory of Rome, Greece, and the Classical Age. Like most historians, they had a particular narrative of the Middle Ages that mattered more than the truth, and they pushed it hard. And subsequent historians repeat that narrative verbatim without considering if perhaps their sources might not be telling the truth. Some of our notions about how the Middle Ages works actually applies much better to the Early Modern period instead--for example, it was during the Early Modern that bathing was restricted because "modern science" (the miasma theory of disease) knows that bathing is how you get sick.
A final point is that there is a particular axe to grind with the question of religion. Many Protestants sought to deny anything that the Catholic pope did. The Middle Ages, being an era where the Catholic Church and the pope had far greater political power than he holds today, then becomes a prime target of criticism. Indeed, this criticism did reach the point that the Christianization of the Roman Empire was blamed for its fall (cf. Edward Gibbon).
I often comment that to learn history, you should first forget everything you learned in school about it. It feels to me that it's more often wrong than right.