Does magnetic coupling cause common mode or differential noise in this case?
It seems like magnetic coupling causes differential noise rather than common mode noise.


In the illustration, that is what is going on.


  On the other hand, I read many places that STP wiring minimizes the induced noise and differential ended inputs are used to subtract the same noise on both lines.


Suppose there's a third wire (ground, for example) connecting the two boxes.

And there is a changing magnetic flux in the loop between the data wires and the ground wire.

This will cause a common-mode (same direction) current on the two data wires. And using a differential receiver means this current won't (ideally) be detected as part of the signal.

If the loop between the ground wire and the data lines is bigger (for example, the ground wire loop may actually go through the building mains wiring) than the loop between the two data lines, the common mode current may be much larger than the current shown in your illustration, so it's a good thing we can ignore it at our receiver.