I solved my problem.
I looked at my quests using the profile editor but couldn't find the IDs mentioned in the warnings. There were a lot of quests from "unknown" though with only an ID as a name. I'm guessing these are old daily tasks.
So I looked into my profile json file directly and found the problematic IDs. They all had in common that the same quest IDs and their counters existed in the pmc section (ConditionCounters, changeRequirement) as well as in the scav section (ConditionCounters, Quests). I deleted all entries of the problematic IDs in both sections and I don't get warnings or the error anymore.
My guess is that the IDs in the scav section are old Fence dailys from 3.6.1 that for some reason share the same ID and counters with pmc dailys. Maybe 3.7.0 changed the way these IDs are generated? That's also why the bug only happened when playing as a scav as I'm guessing the scav part of the json is only parsed at the end of scav raids. Maybe deleting all entries was a bit excessive, I think only the ones in the scav section would've been enough, but I wanted to be sure. As all these quests are dailys so I don't think I broke anything else.