It's less dysfunctional and more weird, but as I was looking at the tempest PrC (Complete Adventurer) for another discussion, I noticed that the tempest defense feature provides a typeless bonus to AC. (Which, among other things, means that it presumably applies both to flat-footed AC and touch AC, I think.)

Are there supposed to be typeless bonuses to AC? Are there any others? It's not a true dysfunction because there's nothing stopping it from working, but it's a noticeable break from what had been established as a pattern that seems to be mostly otherwise relatively rigidly adhered to.