It's been a while since I played any of the DH type games, so I wanted to check with some GM's about something I ran into in my game today. Our GM apparently gave fate points to some of our enemies which I found rather irregular. Has there been a change, or is this just the GM playing fast and loose with the rules?

Enemies with Fate Points have been a thing since the very first iteration of Dark Heresy. Hell, there is a talent called "Touched By The Fates" which specifically exists to grant NPCs the use of Fate Points. Both in the splatbooks and written adventures there are several named NPCs from FFG that can at times even have more FPs than most PCs.

So no, I'd say your GM is just running the game as it has been run for years now, no change or rule-bending here.