That's not what I recall. v2.9 was made with surface-mount pin header sockets.
However, there was a time when there were questions about which capacitors were to be placed in which positions on the boards for v2.5 (back around 2018, but that got straightened out).
And there were some boards from some makers during that period which were found to have been inconsistent with the standard (Jotego uncovered this a few years back), but I don't recall the details off the top of my head - it's in a thread somewhere on the forum.