ToME: the Tales of Maj'Eyal

Adept prodigy will add an additional 0.3 mastery in following cases (if you've already learned this prodigy):
1) get an escort tree (other than tinkers) by saving an escort, resulting 1.60 mastery
2) improve your Antimagic mastery by completing the antimagic challenge when already being antimagic
3) improve your Harmony/Vile Life mastery by eating the (Corrupted) Heart of the Sandworm Queen when already having Harmony/Vile Life unlocked
4) improve your Fungus mastery by saving Derth and reporting to Myssil when already having Fungus unlocked
5) improve your Hexes mastery by siding with the Grand Corruptor and killing Myssil when already having Hexes unlocked
6) improve your Stealth and/or Scoundrel masteries by learning Tricks of the Trade prodigy

I believe these are bugs.

In following cases such bug won't happen:
1) learn and unlock Combat Training, Staff Combat and Mindstar mastery from the respective trainers
2) learn and unlock an racial tree by dying and rising by using Fanged Collar/ Rak'Shor's Cunning prodigy.
3) learn and unlock Cursed Aura tree when unleashing hatre on an item
4) learn and unlock Physics and Chemistry trees from the Ancient Automated Teacher
5) learn and unlock a tree by learning Worldly Knowledge prodigy
6) improve your Poisons and Trapping masteries by learning Mystical Cunning prodigy, even when having them both unlocked
7) spend a category point to improve the mastery of one of your trees and cancel this action in the level-up dialog (though this bug will happen with True Respec addon. a spend and a cancel will yield 0.60 additional mastery from nothing)
8）improve/decrease your masteries by equipping certain items

I believe that this bug is still unfixed in 1.6.7.

Now I've found that this bug is actually not limited to Adept but anything offering "talents mastery bonus". Adept is just the most common one offering this. Other examples include (and not limited to): Ring of the War Master, Radiance and Rope Belt of the Thaloren.

For example: if you save a warrior escort and choose to have access to the Conditioning tree with the Ring of the War Master equipped, you'll get the Conditioning tree at 1.60 mastery. And if you unequip the ring later, you still have Conditioning tree at 1.30 mastery.

For another more extreme example: if you're a Thaloren Wyrmic and have unlocked Harmony with a category point, you can have Fungus and Harmony at 2.00 mastery with Rope Belt of the Thaloren and Adept, without actually equipping the belt!