I think the most common ones are words/phrases like:
仕方ない/しょうがない (It can't be helped; oh well)
すみません (sorry; excuse me; thanks)
そうか/そうなんや (I see; Is that so?)
そうだ(that's right; yeah)
まぁ (well...; meh)
I don't really know what the deal is, but I'm guessing it's happening for me mostly with words that aren't strictly translatable into English and have different nuances or applications (or levels of naturalness) than what you might say in English.
Any thoughts from you expats who have returned home or moved on to another country? Has this happened to you?