The lore was ambiguous about what the Mind Flayer (S2) was. The absolutely worst part is when the lore in S4 established that the Mind Flayer was not in fact, some cool mysterious eldritch god (you know, something strange), but actually just some 40 year old asshole LARPing as a spider using magic dust who also has super powers for literally no fucking reason at all. If you can ignore the lore downgrade, the season's big bad (Vecna) is 50% okay and 50% wtf when did this become a Marvel movie?. The only thing they had to do to unfuck the lore was say "Vecna (some random asshole who has powers for no reason) and the Mind Flayer (eldritch shadow god thing) are working together (for literally any reason who cares)". FFS who cares about some random asshole LARPing as a spider? That's the fucking stupidest shit ever!!! First they're like "As a child, Vecna was obsessed with spiders." Then you're like oh okay, that explains why he's working with this shadow monster who definitely does not look like a spider but close enough for someone whose weirdly obsessed with spiders to be interested. Because if someone was that obsessed with actual spiders, they'd LARP as something that looks a lot more like an actual fucking spider.

Then everything is good to go, until they quickly pull a fast one on you, like they forgot at the last second that someone was going to ask "yeah that's cool and all, BTW what does all this Vecna stuff have to do with S2/S3?" and then they do a quick lame exposition dump explaining that the upside down was just Vecna thinking about darkness and shit found some magic dust and used it to LARP as a spider (WHICH DOES NOT ACTUALLY LOOK LIKE A SPIDER HOLY RETCON BATMAN), and it's extremely obvious this is a desperate attempt to retcon away the "sry kid, we were making it up as we go because netflix demanded with make more than one season" with "wow it was Vecna the whole time!!!"

Then everybody gaslights you that this was planned from the beginning despite originally the show was planned to be an anthology (and S1 plays well as a complete self-contained show).