If you're one spec, level up and train new ranks of skills, the skills on those hotbars are updated to the correct ranks. But your second spec spell ranks are how they were before.

Example:

Spec 1 is Elemental, I hit 80 and get my new lava burst (rank 2). I click train and the skill updates accordingly.

As soon as I switch over to resto, lava burst is still rank 1.

This may not technically be a bug, but a creature comfort feature that was added into the game a while back will hurt people who level using dual spec.

This is currently a known issue, and I do not have an ETA on when or if it will be fixed.

You'll need to remember to manually update your action bars of the inactive spec when learning new ranks of spells.