Missing specialization for some Companions

Any info on this? I completed my rift mage specialization and only the group that joined me had specializations. I

I ran into this problem as well shortly after hitting skyhold.

I had been using the auto leveling for my companions.. but wanted to rebuild them from scratch once their specializations came into play.

I couldn't make the adjustments in Skyhold. So I traveled to one of the camps... and rebuilt them 3 people at a time until everyone was up and running with their new builds.

I thought they may have lost it due to resetting them in Skyhold itself... but it appears to be a bit more complicated than that.

Fairly simple, companions only get their specializations when they leave Skyhold for the first time.  So if you never take a companion anywhere, then they will never get their specialization.  So if you want all your companions to have their Specs then use them in the game.