If your connections has high packet loss, I believe it's possible your hit data won't make it to the server when playing online. i.e. "Rubber bullets." Maybe check your connection next time you're online.
Check lethality settings, as Dux said.
Also possible you're just not aiming as well when your target isn't flying in lazy circles at 200mph. You have to get a good number of hits in the same spot with .50s to do lethal damage. It's possible to rake a target from wingtip to wingtip and not do anything, whereas half the ammo applied to a single point on the enemy would snap a wing off.