I think it's down to the degree that the cap is broken. Cas made a small error and went over the cap a little bit. Wigan went way over the cap.
It's like one club over spent by a few quid and the other over spent by enough for the RFL to have to dock them points.
The 2006 season Castleford only had a small squad and no way did they even reach the cap, never mind go over it !