I used my experienced Pro X. to mind controll Logan and kill of the oppenents Veteran Magneto. He told me that I do not recieve double the points because Logan is not Magneto's nemisis. Do I, or do I not.

As per the FAQ, Mind Control:
As per this entry.... you would get the double points (Arch-Enemy bonus) for Mind Controlling Logan to kill Magneto.

Paraphrased form the FAQs: If a MCd figure KOs a figure, the MCing player earns the points for the KO. If the KOd figure is an Arch-enemy of the MCing figure, the current player earns the points as if the MCer KOd his arch-enemy.

So in short: You do get 2xpoints for Logan killing Mags, if he was MCd by the Prof.

how is logan an archenemy of magneto? logan doesn't have a colored base!

He's not but Prof X is.

Logan is not Mag's AE, but the credit for the kill goes to Prof X, not Logan.