Just got my engine rebuilt, no I hear a noise when I press down on my clutch.
 

After spending $4,400 dollar for a engine rebuild/rotor/housing, I notice the second day I got it back there is a whining sound when you push down on the clutch.
I checked around forums and found out its probably a throwout or pilot bearing. But could it also be just a product of the "break in process"?

Not likely. From your brief description I agree, it sounds like a pilot or throw-out bearing.

I know it's hind-sight, but both are pretty inexpensive and should have been changed (or at least recommended for change) while the engine/transmission is out... if the car has any miles and you have no history of them being changed previously. Now it's going to require the transmission be dropped again. FWIW, I would change both, as well as the rear transmission seal. Consider a clutch fork too. They've been known to fatigue and break with age, especially with stiffer aftermarket clutch kits. It's been a while, but probably < $150 in parts for everything.

Again, it's been a while but probably a little south on prices earlier. Depending on the source probably more like $250 for everything. I want to say the clutch fork is ~ $85-$95, T O Bearing ~$90, Pilot bearing and dust seal ~$40 and rear trans. seal ~ $12.
If you really want to go first class, consider having the flywheel re-surfaced at the same time.
For reference, I've got a lift, the clutch alignment tool, a pilot bearing puller and have R & R'd the FD transmission multiple times. I'm also old and slow and figure it would take me 4 to 6 hours to change everything...not counting the FW resurfacing.

Thanks for the info, And yeah i figured I wouldn't have had to touch the trans whats so ever. The previews owner got a new flywheel, engine seal for there rear, and a rally pro clutch kit put in it by pettit racing in 2010. And the car only has 74k miles on it so I figured I would be good.

I just find it hard to believe there wasn't a error on foul play on the person that rebuilt the engine because the issue started right after I got the car back. But then again I am pretty ignorant about this stuff I i dunno.