I have this issue most often on my medic, though it also effects buffs for engineers and soldiers. Essentially, you put your reticle over an ally, start holding F or whatever your button is to buff the target (or heal them in the case of the medic), and suddenly the game flips out and throws that buff to someone you didnt intend to give it to.

For engineer weapon buffs, this isnt a huge deal - everyone can benefit, and you cant give the buff to someone who already has it. However, the last game I did on my medic today, I was trying to heal one severely wounded player in the middle of a group and I wasted 4 supply pips 'buffing health' on players who were already full. This issue occurs when trying to rez dead players as well - you'll try to target the dead guy and if an ally is anywhere near you'll buff his health instead. It's even more frustrating when you're on your last supply pip and you waste it on someone who's got full health when an ally is incapacitated or low on health.
A similar issue occurs for soldiers trying to resupply ammo to someone who is low on or completely out of ammo, and instead throwing the ammo box at someone who has nearly full ammunition.

The simplest way to fix this, I think, is to give the buffing abilities a priority system. For soldiers, the game should prioritize targets with low ammo over those with high ammo. For medics, it should prioritize incapped players over those with low health, and low health players over those with high health.

Oftentimes, I found it difficult just to get the F to appear to throw a needle to an incapacitated team mate. It has to be at just the right angle, particularly if he's against a wall. I don't bother if they're at a command post - it will go straight through them, pull me in the comm post and switch me to an engie :brokencomputer: Then someone can sprint past and suddenly my camera will jerk around and my character will be dragged after him like a dog pulled off its leash. Very annoying...

I've had this happen too.

Worst I've had was when I was trying to buff a near-dead teammate who was still in line of fire, and I ended up, while I still had the prompt over the chest of the guy I wanted to buff, having the buff hit someone BEHIND me instead. The friend I was trying to buff got gunned down, then I buffed the same WRONG target again, and again while the prompt continued to show on the guy I wanted to revive.

EDIT: I will mention though - it DOES work the way it should more often than it fails, at least for me (I'm on PS3, and haven't played online yet)