This was also a problem in ARMA II.

I noticed that the grenade launcher seems to fire about 20m to the right at 300m as well... and there was no wind.

Seems more reasonable to me, you have to make sure your barrel is not in front of the rocks, remember, you barrel and sights are not in the same place as the gun, the closer you are the more off this will be, depending on the zeroing on the scope. It takes some stance adjustment and going in and out of optics to get it right, so I don't think it's a issue.

This is actually a real-life issue. When I was in the Army, a friend of mine was on a range shooting at targets from behind a HMMWV, long story short, he was aiming at a target over the hood and put a round into the hood of the HMMWV. Just think of it like this: You could put your hand over the barrel, and wouldn't know it was there looking through the sights. Muzzle awareness is the name of the game.

Yeah exploited, this isn't a arcade game where your sights are actually a camera inside your barrel, you have to check where your barrel is while using stance to get your barrel up juuuuust enough, best way to do this is quickly switchign in and out of optics.

Also, keeping barrel awareness is really important if you're doing a bounding fire line(where your standing up and a freind is kneeling in front of you, I think that can be used for lots of bullets down range, not sure if there's any oter use for that stance.)

Real World Issue. You have .5" to 3" of elevation between your optics and the bore of your rifle, depending on rifle/optics/mount (Ruger 10/22 vs AK47?)

This is as intended. Check your barrel before you aim down the sights. If you have the crosshair on, it will show when your barrel is obstructed by cover.

Real world proof of this problem happening, it's not just a video game problem folks! Ref http://www.theblueflyer.com/Blue%20Flyer%20html%20folder/Police%20Marksman%20Rodirguez.html

Albuquerque Police Marksman Steve Rodirguez peered through the scope of his high-powered rifle targeting Mexican national, Miguel Antonio Dominguez-Flores, who was trying to make an escape from a foiled bank robbery.

On November 7, 1993, Dominguez-Flores, 45, the director of a Mexican technical school, held up the United New Mexico Bank branch at Montgomery Boulevard and Pennsylvania Street in Northeast Albuquerque.

He held a handgun to the head of a bank teller he took hostage just outside the front doors, as he tried to negotiate for a vehicle after police officers rushed a side entrance forcing him into the parking lot. (APD Records, 1993)
Dominguez-Flores told Deputy Chief Nick Alarid that he also had dynamite wrapped around his body.

He did not have a bomb.

Officer Rodirguez fired.

Dominguez-Flores pulled his head up looking for where the sound came.

Rodirguez was surprised that he missed and fired again.

Dominguez-Flores looked around but did not harm his hostage.

A former special weapons and tactics team member, Patrolman Bobby Vasquez who responded to the call noticed that the barrel of Rodirguez' rifle was aimed at a wall about 15 feet in front of him while the scope mounted several inches higher allowed the sniper to see his target clearly.

The first two shots had struck the wall.

Vasquez radioed Rodirguez telling him to straighten up and try again.

Rodirguez fired again and Dominguez-Flores fell instantly dead from a shot to his head.

Yes the principal as as expected but the effect is extreme. Optics are mounted only two or inches above the 'boresight' but in A2/3 it would seem more like 6 inches.

I understand that the barrel is below the sight and I take this into account but I can be pretty well clear of the rock and still hit it

Honestly, I doubt you took into account that the barrel is below the sight.

A - You claimed you were hitting the rock despite having a clear picture through your sight. As I and others have stated, these two do not correlate with each other

B - I have never had this problem. I've taken cover behind plenty of walls, rocks, and windows, and I've only hit my cover when I wasn't high enough. A minor stance adjustment would allow me to fire free and unobstructed. Judging by the votes as well, this is not an issue many others are experiencing. It's possible it's a bug that only affects a few, but I personally have never encountered any problems with being "pretty well clear" of an obstacle and still hitting it.

Yes this does happen in RL but A3 hit boxes are a little jacked atm so it's possible it's being exagerated. I, however, just tried hitting rocks (and other objects) both by aiming at them and otherwise and it appeared that my rounds were just going threw them so... I cant hit anything even if i try apparently

This is by design, not a bug - bullets are emitted from the gun barrel in Arma3.

Closing.