I put a music CD on top of my microwave oven (by mistake) and then used the microwave oven to heat food. Has the oven's magentron done anything to damage the CD?

I have a stack of CD’s next to my microwave, and haven’t noticed any problem.
Doesn’t the CD play now?

If your microwave oven is operating properly, I don’t see how it would have any effect on your CD. Play it and find out.

Yeah – play it and see.

CD’s don’t store info using a magnetic media, they store it using physical pits in the disc that are read by a laser. If the microwave got hot enough to melt the plastic of the CD then it may stop them from being read but I doubt the top of a microwave even gets that warm.

Why not just try playing it?

exasperated sigh

The question might be about more than immediate damage that would be evident on a first playing. It could be that @elbanditoroso is asking whether the microwave could have done the kind of damage that is unnoticeable at first, but gets worse over time.

It shouldn’t. As some jellies mentioned above, your microwave should not be leaking anything that would cause changes in anything.

Microwave ovens are shielded, they don’t emit (much?) radiation.

To test the shielding, unplug the microwave oven, put a cell phone in the oven and close the door.

GIve it a call. It won’t ring.

DO NOT TURN ON THE OVEN WITH A CELL PHONE INSIDE!!

Your CD should be fine.

Outside the microwave? No.

CDs are optical and aren’t affected by magnetism, microwaves, radiation, or anything else like that. A bright enough laser will erase the information on a rewritable CD, but there’s no lasers in a microwave. If you put CDs on a hot surface, they’ll melt, but the outside of a microwave doesn’t even get warm.