Terrible understanding of science in the medieval period probably has multiple origins, but I want to just point out two places where bad historical ideas about medieval science were mobilized:

• During the 18th-century Enlightenment, the idea that the philosophes had created a new, scientific world that was a harsh break with the mystical, alchemical, and religious past was part of their definition of what "Enlightement" meant, but was heavily based on an exaggerated notion of what pre-17th century work was like (and also exaggerated the "scientificness" of some of their heroes, like Newton, who was mystical, religious, and an alchemist).

• In the 19th century, the idea of the "Conflict thesis" was promoted by various supporters of science in the US and UK, arguing that religion and science have always been at war, and claiming that religion was responsible for the suppression of science in the medieval period. Again, this was done for the rhetorical needs of the 19th century: to promote, in their mind, the proper understanding of science and to make an argument about how different the "modern" period was from what predated it.

In both of these cases you can see that creating an imagined idea of how terrible things were in the past with regards to science, and playing the blame on "non-scientific" forces like religion, were used to make rhetorical arguments about what it meant to be "modern" and "scientific." And in both cases, it is worth emphasizing, these are very poor historical accounts about what science was like, not only in the medieval period, but in the more "modern" periods as well (religion and science have never entirely divorced, for example).