Happens all the time, all the gear and kit people run can pretty much block out a bb hit so usually the best thing to do is just call a hit when you think you've been hit but you're not 100% sure. It's usually faster to go back to spawn than argue w/ some guy for 5 mins.
Of course there are exceptions, a lot of times people will think they hit you when in reality they don't have the range, miss, or can't shoot through foliage (often times this happens w/ newer players who don't know the actual range and performance of their guns). In that case I usually keep playing until I actually get hit. On the reverse side, if you're not sure you're hitting someone, move up and get a better shot. If you can't see your shots, there's a good chance you're missing. If you're hitting him he'll call it eventually (unless they're cheating, in that case find a ref and let him know).
Gun hits are gun hits, call it and depending on rules keep playing or switch to secondary. If you got flanked in the process then kudos to them for getting into position to take you out. It's the nature of the game.
If someone is arguing/yelling at you for not calling what they think was a hit and he gets aggressive about it, go find a ref and inform them. It happens from time to time when some guy takes the game too seriously.
Regarding ranger11's tip about shooting the guy w/ a secondary... while it might work for him, I wouldn't recommend it over finding a ref to remove the guy from play. It's a bit confrontational and likely to start a fight.
Just your friendly neighborhood narcissist gearwhore.