I think it sometimes is on purpose
I've had two sets of flights on Emirates in First and Business Class on a First Class ticket. For all 7 segments I gave them my United number and it printed on my boarding passes. Not one of the segments credited! For an airline that prides itself on customer service and quality, this is pretty bad.
For the first 3 segments, I had to fax the boarding passes in. Now United changed the rules and I have to send the originals in. I think it's an annoying element. It seems like the international carriers are worse at complying with automatic credit.