Some noise is normal, since the engine and flywheel/pressure plate are indeed spinning, whenever the engine is running.
It would probably be hard to tell if the noise you're hearing is the pressure plate, clutch disc, or the flywheel by sound alone. Any of them can cause noise from the transmission for a variety of reasons.
The pressure plate bolts can come loose if they weren't torqued to spec when it was installed, and then you'd get a loose flywheel and/or clutch disc that has extra room on the splined shaft - though I would think this would present issues with shifting that you'd feel when driving and the clutch pedal not disengaging the clutch like it should.
The flywheel can also come loose if the bolts holding it to the crankshaft weren't tightened correctly.
There can also just be general balance issues with the clutch disc, pressure plate, or flywheel, since they are all balanced with weights, and if one of those weights comes off, it can unbalance the whole assembly, or just that one part enough so that it wobbles slightly and makes contact with the other balanced parts.
There is an access hole in the manual transmission, with a rubber stopper in it. You could remove that stopper and peer around in there with a flashlight (be sure the parking brake is on and the wheels are chocked before getting under the vehicle!), to see if any of the balance weights are in the bottom of the transmission housing.
I'd also suggest listening more closely to the noise and figuring out more of when it does happen/doesn't happen and any other causes and effects - you could even leave that rubber stopper out and have the engine running and listen for it from outside the vehicle (again, with parking brake on and wheels chocked for safety - might even be a good idea to have another person in the driver's seat to step on the brake if you're going to be sticking your body and/or head under the body to listen closely with the engine running).
If you don't notice anything other than the spinning sound, and there are no drivability issues, it might be something to stay aware of, but not worth taking it in for or bothering the mechanic about. Checking the clutch/pressure plate/flywheel, other than through the access hole, involves dropping the transmission the same as a clutch job, so unless the mechanic is willing to drop that transmission just to re-check the work and/or discover why you're hearing the spinning sound, your best course of action at this point might just be to stay aware, and keep alert for any new noises or change in clutch performance. You could always just take it by and have the mechanic or the shop listen to the noise and make a note of it, just so later on if something does happen that requires them to re-do the work, you're covered in terms of having brought it to their attention as soon as you noticed something.
