This problem happens only after the "tea event" update.
I'm playing on steam so I'm not sure about other versions.
The three type of collect quest :
- Collect Mutagen
- Collect Fossil
- Trait upgrade
They seems to determine the value of the player current have, and not the increased value.
So it result in those mutagen and upgrade quest completed automatically after I do a reset, and the fossil one's value will be same as my fossil currently have.