So loaded up today (after fixing the save with the hotfix. It took me a while to notice the missing skills on my action bar...but I also seem to have gained the broadside skill. And no, I am not a pirate in any way. The missing skills I mentioned weren't gone, they just dissapeared from the action bar and needed to be re-added. Broadside though is completely out of left field.
I had this bug as well. It occurred before the teleport bug, but I ended up with that as well. The wrong skill replaced "The Cure" from emomancy. I could use the skill that was on the bar even though I did not have the skill tree. However, if I went and changed the hot button for the false skill to something from my list it would be removed, and then it would not appear in the options for other buttons (good). Just wanted to add the details of my experience in case it helped with the bug. Thanks for a great game, hope the new bugs get ironed out soon!