Well the hardest for me to wrap my head around Conceptually are super speed, super strength and healing factors.
Super speed: This has to be the toughest for me. I can envision someone running around 200 mph or so. But this thing where people are moving and reacting at super sonic speeds or higher is crazy. How do they navigate? And if somehow they're able to process information fast enough to react, then their perception would be normal. So running from LA to NY would be real time for them. That sucks.
Super Strength:
I can rationalize 100's of tons. Afterall, we have things in the real world like ants and rhino beatles that lift like 10 times their own body mass and such. But when we get into thousands, hundreds of thousands or -in some cases- millions of tons, unaided by psionics or some other non physical force i.e. gravity, Then I just can't feel it.
Healing Factor:
This one is just plain dumb in some cases. I can dig it to a certain degree, however, when people are coming back from getting blown to pieces or reduced down to mere skeletons, that goes beyond healing factor and into metaphysics because those are resurrections IMO.