The levelling up mechanism for AoPc is a little tricky. In theory, you get one level up for every 2 dungeon levels, but special levels are counted somewhat differently, giving you bonus clevs.
It's actually per three floors, although this condition starts on dlvl3. In a typical game, you should hit clvl9, leveling at 3, 6, 9, 12, etc. If a special level exists on one of these floors, you will ALSO get a level for the special level as well. This means you can get extra levels for the following:
Hell's Arena spawning on dlvl3
Chained Court spawning on dlvl6
The Wall/Hell's Armory spawning on dlvl9
The Wall/Halls of Carnage spawning on dlvl12
Spider's Lair/The Vaults spawning on dlvl18
The Vaults spawning on dlvl21
This leads to a potential of clvl15, having more traits than you could possibly know what to do with. Given an amount of luck on the first couple of floors, you may end up leveling early by enemy friendly fire, leading to a clvl16. (I assume this is how you managed clvl13 in spite of only 11 floors' worth of level ups.)
Are the extra levels of traits supposed to be selectable at Level 12 or after? Being able to select Ironman(4) upon reaching level 12 saved me as well.
This is intentional for basic traits only: those with a normal max of two ranks can go up to three, and those with a normal max of three ranks can go up to five. It makes YAAM'd runs on higher difficulties and A100 far more amusing.
Congrats on the Pacifism Plat! Not an easy run at all, even if you weren't aiming for the Diamond. Best of luck on other Nightmare! victories, I highly recommend AoMC for best results.