The Non-Euclidian Staircase

Some degree of this is pretty much unavoidable, at least if you manage to make the NPCs attitudes differ from yours (and I do hope any "bad guys" you GM are this). Most of us simply aren't the sort that would do what the worst of our antagonists will do casually.

But, also, some 'leakage' is inevitable. Several ideas commonly accepted in historical settings (slavery, arranged marriage, murderous xenophobia) are rejected by or even abhorrent to the modern-day American/European mind. Also, modern military, economic, medical, and social theory revolutionize basic assumptions of, say, medieval life. Finding a player willing to line up in ranks against cannon fire, or to subject to bleeding for treatment of a fever, or to simply acknowledge that class mobility doesn't exist is a severe challenge, and remembering that NPCs should think that way is just as much a challenge.

I actually work with this as a source of story and conflict in my bronze age fantasy setting, as I have three distinct cultures (well, two full cultures and one "border" group that tries to mix the two, picking and choosing when they conflict), each of which follow rather distinct reasonings to get to their "cultural norms". The two major cultures end up at opposite extremes often enough that conflict is inevitable.

Day-to-day, I try to have this impact even little things... For example, the casual domestication of small animals as pets is not practiced in this setting (for reasons I won't go into here). This tiny difference has all sorts of ramifications in behavior and attitude, not to mention linguistic influences (describing people with animal-like traits is rare) and economic impacts (preserving grain rodent-free is more difficult without cats, for example).

The hardest part about being alien, though, is being consistent. I have problems myself with slipping up and letting a modern assumption color a decision, and I'm still in the world-design phase (with only 3 people having actually played any significant time at all). Being appropriately alien is great, and it gives the game a good feel... but it's also work.