Pretty common. Joining a group of 4 other random pugs and queuing together provides a good bit of defense against this (sometimes the game will still decide 2 of you need to join a completely separate match.)
The less popular maps (anything but cracked planetoid and capture and hold) also tend to have this problem more, I think. People will see the queue for cracked planetoid become available, join it, but they're still queued for solar wind, which they didn't really want to join anyway. Their faction starts with 1 less player when solar wind becomes available. (At least, I believe that's how it works.)
Also, the 5-player minimum capture and hold starts at 5, then fills to 10, so if one faction has more players waiting, things can get unbalanced really fast.
Thanks for the replies. At least now I know it's not just me.....lol I hope they find a fix as I really enjoy PvP when the numbers are even close to equal. 10v2 just isn't a lot of fun no matter which side of the equation you are on.