There were a period where they were really having visible scaling problems, with response times often getting painfully slow - apparently especially due to slow I/O. These problems completely disappeared after their move to Rackspace's managed hosting.
Now it looks like they might be hitting a new barrier that might require architectural changes to overcome.
There are an infinite number of reasons an app could fail at any given moment. Just because we see the same "something went wrong" page 4 years later doesn't mean we're seeing the same problem, or even the same class of problem. It just means that the sun still rose in the east this morning, my stupid car will probably have something new wrong with it when I leave my apartment in a few hours, and software is still really, really complex.
The GitHub team is a smart bunch. I highly doubt they're still dealing with the same class of issues that plagued them four years ago, and it just seems kinda strange to even bring it up.