PWM Brushed DC Motor Noise
It is normal, because \$i_c=C\dfrac{du_c}{dt}\$. You are doing PWM, so \$\dfrac{du}{dt}\$  is very high and the current spikes go to infinity. 
Not an expert here, but I do think it has nothing to do with CE.
You can install additional chokes on both lines to limit \$\dfrac{di}{dt}\$ You can use also a common mode choke that will turn into differential mode if you connect forward and return wires. It has to provide 1% to 3% voltage drop, but you should use a function generator to check for resonance. The PWN frequency have to stay below the resonance frequency.


EDIT:

A rough calculation gives me a two very tiny inductors in range of 2 to 5 micro henries. Without a motor connected, omitting the cable capacitance, then supposing you have 2 x 2.2uH and those three caps of 0.1uF you get:


Equivalent capacitance 0.1uF + 0.1uF/2= 0.15uF
Equvalent inductance 2 x 2.2uH = 4.4uH


$$f_r=\dfrac{1}{2\pi\sqrt{LC}} = \dfrac{1}{2\pi\sqrt{0.15\cdot 4.4\cdot 10^{-12}}} $$
$$f_r\approx 196 kHz$$

The resonance frequency does not need to be very far away from your PWM frequency, 30kHz would be good enough.

Doing tests you can protect the motor/cable/caps/driver from overvoltage with fast diodes. This will prevent the oscillations building high voltages.







simulate this circuit &ndash; Schematic created using CircuitLab