Weapons do not currently allow for "sacrificed DPS" - this means that caster weapons will appear to have a lower expected ilevel than they actually do, and will have a higher ilevel than they actually do.
Shields do not currently properly calculate their AC/block values
It seems that "increased base armor" has a different modifier than "additional armor" (if that makes sense), causing "additional armor" to pump up the value too high to make those items balance. Items with unnaturally high AC aren't going to get the right ilevel at the moment.
Ranged weapons, wands, and fist weapons currently aren't in.
Experimental vendor value estimation is in for blues, but it's not terribly accurate.
Druid-specific weapons are screwy, since they have form-specific bonuses. This makes them calculate out as overpowered.
Calculated armor values won't always be dead on, but will be within a few points.
Calculations and concept based on Hyzenthlei's wonderful work, found here. Code and stuffs by Adrine of Cenarion Circle.