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Add a capacitor or capacitors between the input of the 5V regulator and ground. See the regulator datasheet for the recommended value(s). C1 and C2 don't count because of the diode you have between them and the regulator.
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I would insert the inductor in the supply line to the motor controller only, and then move C1 and C2 to the motor controller side of that inductor.
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However, I don't think it will make much difference. The inductance of the motor is probably much greater than 100uH.