I just found something that doesn't qualify as a bug technically, but is a bit of an annoyance.
I fell into a quest trap that few seem to encounter. Apparently you are supposed to stumble across Fort Emerald before you find Fort Saffron. This leads you to get the Wyrmkin Tails quest from Beadle. Then eventually you are supposed to be allowed through the barriers and up into the areas that lead to the Wyrmkins and the Drake and its brood. It may seem simple, but things didn't go that way for me.
I wasn't able to find Fort Emerald before I found Fort Saffron. So I figured I would come across the former eventually while exploring and went off on the jobs and quests for Fort Saffron. I get through the bandit hideout that led from the Fort Saffron jail, and eventually out into the valley where the Wyrmkins were.
I naturally set about eradicating them thinking they were a pest. Then I came across Fort Emerald and had to dispel the barriers to get in, which I thought was a bit odd. I got the quest from Beadle and went out to find some thinking they would regenerate like everywhere else in the game. I discovered to my horror that the Wyrmkins were permanently gone.
Being an avid "Game saver" as I am, I saved around the time I found Fort Emerald. I can't help but feel that three things SHOULD have been inserted in the game here. One, the Wyrmkins should have been made to regenerate like other animals in the game. Two, upon approaching the barriers at Fort Emerald, you should have come in contact with a guard or the person in charge in some way. Three, the valley shouldn't have been made accessible to Fort Emerald from the wrong end to begin with.
Oh well. Nothing I can do now. It's just one job that will never be completed.