It might be the PWM that makes problem but often its the brushes in the motor that causes the disturbance (sparks during operation). Test if you still have the problem with a resistor instead of the motor. If the problem is gone with resistor then it's the motor. And YES, this is a EMC issue.
Try some filtering on your DC motor by adding 100nF capacitors on it. That means from DC+ to motor case and from DC- to motor case (known as Y configuration). Very important: As close as possible to the motor with leads as short as possible! Solder them direct on the motor. If this not help add another 100nF between + and - (known as X configuration) and also a inductivity of a few µH in the DC+ and DC- wire (this can be a wire that goes a few times trough a small ferrite torroid).
Edit:
"As my teachers always said, EMC is magic......."
-> capacitors and inductors are the magic spells!