Happens to my wife and I all the time.
If you are not upgraded prior to 3 hours and end up on the airport check in list for upgrades--it does not necessarily keep everyone together.
Since it is a combination of automated and gate agent controlled, it seems to split passengers.
Same ridiculousness when my wife and I upgrade and they give us a window and aisle seat in different rows even if there are plenty of empty seats.
They just do not care about anything that does not bring revenue to them at this point.