I was denied entry to Japan once, even though I am a US citizen and therefore visa waiver eligible.

I was coming here for grad school classes, but either the university or the justice ministry screwed up some paperwork for my visa (apparently my name was misspelled), so I was told to just come in and have everything settled on the ground. I explained the situation to the immigration officer and was promptly taken off to detention for a couple of hours, during which time I was formally denied entry and then told (by a friendly immigration officer) to write an appeal in longhand. The appeal was granted while I waited, and I got a "special entry permit" in my passport which was good for a year. Apparently they were not procedurally allowed to admit me as a student without a visa, but they had more leeway to make a determination on appeal.

In the detention area, I came across several Asian and Eastern European tourists who were trying to transit without visas, as well as an American guy who had apparently been deported in the past and was trying to get back in; his case required an overnight stay at a guarded hotel room in NRT.