There are several problems associated with the use of subsonic ammunition in gas operated, semi- and full automatic weapons, and even occasionally in bolt-action weapons (see "phosphating").
The first and most important is that since the action is closed by means of an operating spring, the cartridge may not be seated fully forward in the chamber. This commonly causes a failure of the cartridge case to obdurate (seal) and the propellant gasses,especially in the very tapered 5.56mm cartridge. Instead of pushing the projectile out of the bore, flow back by the cartridge case, usually sticking the projectile an inch or so ahead of the chamber in the bore. The danger of this condition is obvious, and it is therefore of utmost importance that the operator pay attention to each round, ensuring that the projectile has left the bore - indicated by impact sound. The indicator of failure to obdurate is a slight but audible "hissing" sound as the propellant gasses flow back by the cartridge case. Also, the cartridge case will have a "smoked" appearance at the forward edge, back to the shoulder area. The very tapered profile of the 5.56 cartridge case lends itself to this failure mode, although it has occurred in some chambers, usually with an out-of-spec throat in .308/7.62 as well.
The correct procedure to avoid this pitfall is to give the Forward Assist a sharp rap prior to firing each cartridge. This ensures that all bolt/carrier parts are fully forward as well as the chambered cartridge. Whilst the AR-family of weapons does have a safety cam on the firing pin, this safety is designed to prevent firing of the weapon with the bolt in the unlocked position (with high velocity ammunition) and does NOT prevent firing with the parts not fully forward and fully locked. Another way to ensure full chambering, particularly in those weapons which are not provided with the Forward Assist is to short-load the magazine by several rounds, thus lessening the amount of force spent by the operating spring/buffer in stripping a round from the magazine and increasing the amount of force it can spend on chambering the round.
The second undesirable condition present in gas-operated firearms is the presence of the gas bleed hole in the bore. While this does not prevent the use of subsonic ammunition, since SSA uses much less propellant than high velocity ammunition, the presence of a bleed-off does tend to produce more velocity variation and thus vertical stringing of the shot group than that found in a solid bore.
The third and perhaps most relevant problem we have found in gas-operated firearms is the presence of phosphate particles inside the bore of both gas-operated and other action types which have received an outer phosphate finish to the barrel. This problem can cause projectiles to fail to exit ( Think of the subsonic projectile hitting a grappling hook with a parachute attached on its way down the bore) This condition has become more prevalent in the last few years. It is caused at barrel manufacture by the phosphating processor failing to seal the bore whilst the phosphate coatings are applied to the outer barrel surfaces, and has been observed in some of the most and least expensive of firearms. It is plainly visible through a good quality borescope. Shooting high velocity ammunition will not remove these particles. EBR is currently working on a relatively inexpensive solution, and in the future will warrant the use of its ammunition only in barrels to which this solution has been applied (thus ensuring the absence of phosphate particles in the bore. The cure has the added advantage of assisting in good accuracy, even with the use of high-velocity ammunition.
Finally, subsonic rifle ammunition will not work in a firearm which has a fluted chamber (NOT barrel). This fluted chambering is typically found in delayed-blowback firearms and is put there to purposely direct propellant gasses back past the fired case to help "float" it out of the chamber and prevent case sticking in high-velocity ammunition. Obviously, it can cause subsonic ammunition to fail to obdurate (seal the chamber) causing a failure of the projectile to exit the muzzle. Subsonic rifle ammunition SHOULD NOT be used in this type of firearm for this reason.
The above conditions do not necessarily prevent the use of subsonic ammunition in a gas gun, but do impart on the operator the responsibility of carefully monitoring the effect of these conditions in his/her particular firearm. As always, any ammunition carried needs to be tested in the firearm to be carried prior to any operational use. This is just good common sense.