Never been rejected - it's either full or one of those reservation only places.
Also, if it's later in the evening, make note of the last order time and not the closing time.
If LO is 10:30 and you show up and 10:31, you won't get seated even if they don't 'close' till 11pm.
Concerning this situation, it always makes me chuckle when people living here say things like " Well it hasn't happened to me" so therefore it doesn't happen. No context at all. For all we know, the person spends all their time hanging out in Roppongi or around the city in places that are foreign-friendly or that see a large foreign clientele.
It totally does happen. And not for language reasons, because it's crowded, or whatever other reason...
I'll give you two examples from the not so distant past:
1). I sometimes drink with a doctor friend in Kichijoji, and we were talking about good yakiton places in West Tokyo. He told me that, in his opinion, the best place was a shop in Kunitachi, and told me to go there. A while later, I was in the area, around opening time (5:30), and decided to check it out. The place was an older shop, sort of Showa-era, open entrance on street level with hemp noren so only the lower half of customers entering could be seen. I started in and heard the master shout "Irrashaima........." and as I came through the noren and he saw me it was "Irrashimas.........ahh ah ahh ahaha CLOSED! CLOSED! I was a bit confused and said--"It's only 5:30? You're closed?" The place was an old school yakitori shop, an open place with a U shaped counter with the master behind and only a few younger salarymen along one side. "CLOSED!!! CLOSED!!!" he shouted. I shook my head and headed out, and as i did, the salaryfucks sniggered. The fuck. It was not booked, it was not closed, it was my first time there, and it was very clear that they didn't want me there. Language was not at all an issue.
2). I went to a bar in my neighborhood---a place I'd been before and had simply sucked down a quick drink and left----always with a woman behind the bar. No issues. Came, drank silently and left. One night, I walked in and a guy was behind the bar. As soon as he saw me, he threw up the flying X and screeched "CLOSED"
"Really???"
"CLOSED!!!!"
OK, and as I walked out, this total hipster chick, in the most snide, condescending tone you can possibly imagine said "Byeeee Byeee!" Really? Do you need to rub it in?
Thing is---I don't care. I don't let things like this bother me too much---for every place that refuses customers, there are thousands of places that don't---and if a place doesn't want me, I don't want to be there---I don't argue, I just leave.
But it annoys the fuck out of me when people say that it doesn't happen. It does. Again, it isn't due to closing times, reservations, language troubles, or any other crap apologists want to throw up.