First off you can't be doing any thing wrong just trying to take your wheels off. Hubcentric wheels should have reasonably tight tolerances, obviously two have less than the others.
I have a set of Fikse's that are are a pain to get off. You have to really rock them back and forth to get them off the hub.
One thing I do use on the interface between the wheel and the hub is a very thin coat of Wurth LM 508 anti seize. If you use spacers this really helps getting them off.
If you have a ridge that is making the rim too tight use a 220 or higher emery paper to make it smooth.
Again the wheel interface should be tight but not irremovable.
Max
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