Are you sure you had all the passives maxed out before the patch, @AwesomelyWicked?
Another way to reconcile skill points is load the Ulrich's Skill Point Finder add-on and check the add-on skill point totals against what you get refunded at a respec shrine.
Yeah, I actually checked a few days prior to the launch of Greymoor and had entire skill line maxed out. Unfortunately I play on xbox one and I dont think I could use that add on. Which sucks cause I'm all about getting every skill point available, especially my main. I have seen someone else who had this same problem. Thanks for the help though, may your swords stay sharp!!