As I understand it, IFF works by having a particular aircraft send out a signal at a specific frequency which allows other aircraft to identify it as a friendly. Can this be easily jammed or confused?
My guess is that many opponents of the F-22 will attempt to reduce its stealth advantage by trying to jam IFF transponders and making it tough to distinguish friend and foe. This will of course make BVR kills much more difficult. I know that during the Gulf War, we had some issues with this.
There was an incident in which an Eagle driver fired a Sparrow and then saw the dot on his radar change, identifying the target as a friendly. Fortunately, the target ended up being an Iraqi MiG-29 and they were able to ID it before it was taken out.
IFF isn't the only means of determining friend/foe. Between the elaborate ESM suite, and NCTR modes of the radar, as well as third party targeting info, the Raptor will enjoy a lot greater situational awareness than was available in 1991.