(1) Amtrak does overbook by a certain percentage on a lot of routes. I think it's 3-4%, but I'm not sure.
(2) Usually the "issue" resolves itself due to turnover and you only get overbooked passengers on a few high-traffic segments (PDX-EUG would be an example of one on the Starlight).
(3) With that said, some folks end up in the cafe for 15-20 minutes not because of an overbook but because of trouble finding them seats quickly. Basically, at some high-turnover stops (ABQ comes to mind on the Chief; Minneapolis on the Builder and Denver on the Zephyr come to mind as well), some passengers will get directed into the cafe for a bit while the conductor finds out where the empty seats actually /are/, since those can end up being scattered in ones and twos in odd places and/or wind up "hidden" behind a passenger with an aisle seat.
I ended up in a cafe ABQ-FLG once...the conductor could have found a seat for me, but I asked to remain since most of the ensuing time was taken up by dinner and I didn't want to move my bags again. It has also been known to happen on NE Regionals at travel peaks, though in cases like that where a corridor train is involved, it usually involves underestimating the number of multi-ride/monthly ticket riders who will be on that train.