I don't see what's wrong.
You have 7.77 magic penetration from runes and 8 magic penetration in game. It rounded off the decimals. You have 16 ap from runes and 28 ap in game. The other 12 comes from Masteries (+0.89 per level from Mental Force at level 5 = 4.5, +6 from Arcane Mastery, +1.325 from Archmage (+5% of 26.5)) You have 44 armor in game. Katarina naturally has 37.7 armor at level 5, plus the 6.37 armor from your runes = 44.07 armor.