Could accidentally keeping a wallet with a magnetic money clip in the same pocket as my smartphone potentially cause any perminant harm from the magnet?
Phones have no magnetic media, so no. A magnet on the phone, if it's a Samsung Note series, may interfere with the S-pen until you remove the magnet from the phone. (And the magnet will definitely mess up the calibration of the phone's compass, but so will almost anything metallic, which is why you have to calibrate the compass every time you use it.)