I have several upgrades where somehow I don't have credit for the pre-req upgrades and at least one I know I paid for but don't have credit for. Using the encyclopedia here are my findings:
- Under learning, I have NONE of the Speed 1 through 3, but ALL of the Speed 4 and 5.
- Under Perks, I paid for "Ancestral Nostalgia 1" and it's not showing I have it. (And yet I have version 2 of the same perk, which it presumably only offered to me once I'd bought version 1.)
- Also under perks, I mysteriously don't have credit for Snapshottery (which I believe I got because I had previously learned the skill) but I can take pictures all I like with my camera.
When repairing things about every other bag in my inventory jumps in scale a bit like this:
- Repair bar 10%, bag size 100% (the icon for the bag itself.)
- Repair bar 15% (next step up), bag size 90%
- Repair bar 20%, bag size 100%
- And so on. Seems to only effect every other bag.