No matter how many times I replay level 3 of Trine 2, no matter how many times I uninstall and reinstall, verify the game files, delete my save and start over, I keep coming up short 2 XP whenever I complete this level. And yes, I do use a video guide to ensure I don't miss any locations.

Can anyone tell me how to fix this issue?

Were you perhaps playing on Hard difficulty? There is a known bug in level 3 Mudwater Dale where 2 monster EXP are missing, if played on Hard difficulty (and sometimes with Hardcore Mode on). We haven't figured out why this happens exactly, but turning off Hardcore Mode and setting the difficulty to Easy or Normal and then replaying the level should help. You can turn Hard/Hardcore back on after completing the level and gathering the EXP.

- Aura, Frozenbyte Support