The movie never makes a point to show anything but villains. From Renaissance Vulture to *EVERY* emphasized cage in the Spider-Society, the anomalies are villains. The movie never makes it a point to establish anything to the contrary. 

At what point in the year and a half did it start targeting villains rather than Spider-People? It seems like it happened pretty early, going by the creation of the Spider-Society, but why?

The reason I bring this up is, because the only thing we have to go by is Miguel's statement "You left a hole wide enough for guys like him to get randomly shot into the wrong dimension." Again, if it truly is "random", why have they all been villains and instead rather civilians or random objects?

Weirdly enough, it only ever gets discussed again when Miguel confronts Miles. Just not into deeper detail than him being in the wrong universe where he goes, because of the spider bite.

Yet, E-1610 is seemingly stable, which can't be said about Vulture's visit to E-65. His presence's disturbance was pretty immediate and volatile. Not only on him, but on the universe itself. Something that has only been evident in the first movie when involving the collider, but not the Spider-People that came from it. 

I don't know whether to chuck up the immediate glitching of E-65 to the present instability due to the "hole in the Multiverse" as Miguel claimes or something else entirely.

I'm curious to hear your thoughts on this.

Why are all anomalies Spider-Man villains?