From my experience, there are some people who expect MCU properties to just constantly reference each other, and so people started to "theorise" they were separate when the Netflix shows didnt just constantly reiterate the plots of the latest movies.
This view got a bit of merit when Endgame came out and the shows got immediately cancelled. As someone who views the shows as canon myself, I can admit that the fact that AOS and Runaways occur during the snap and its not mentioned is a bit awkward. But those discrepancies are common in the comics because keeping track of shared universes is really hard.
Over time its become so ingrained that the show are "definitely not canon" that people just cant accept otherwise, so now they have to come up with more convoluted theories to cover up the gaps rather than accept they were wrong.
It really shows the power of echo chambers to ingrain a tightly held belief about something