I've used both in my ARs with no problem and I use mostly fine ball powders...If you set aside accuracy quests, the main concern about using a standard primer in an AR, or other semi-autos with 'free floating' firing pins is the potential (not probability) for a "slam fire" when dropping the bolt carrier group on a live cartridge....
In all of my shooting with an AR, I've only personally known of it happening one time and that was at the DPMS 3-gun match in St Cloud MN in 2006 and it happened to a friend of mine...It disqualified him and he lost about $1,000 (entry fee, travel, etc) due to the Accidental Discharge rule..
Is it a major concern??? not in most cases, but it can be a problem in some instances..When you release the BCG to chamber a live round, extract the round and look at the primer.. It's' not unusual to see a very small dent where the firing pin has struck it...just not hard enough to ignite the primer...
The difference between the standard and magnum primers is the thickness of the primer cup and therein lies the potential danger...
I do, however, seem to get better accuracy using the magnum primers in my AR ammunition that I reload..