Question about Defender of the Crown
 

I just completed DotC and found that when I went to the second area (the elf lands) there where undead heroes. So I loaded a save file to grab some anti-undead and next time I went there there where humans and giants! Tried this again and found out that doing different things altered the heroes you encountered.

I know that at the beginning you can choose your enemy but changing it in the middle seems like a bug.

Another thing I found is than while playing as a Paladin I had the skill Holy Armor in my Paladin tree but in March of the Orcs that skill was given to me in the Mage tree (playing as a Paladin). Is that another bug or are there some differences between the 2 campaigns?

It's not a bug, game world in DotC was designed to be as random as possible to pose a challenge for experienced players. AFAIK, skill trees differ between 'Orcs' and smaller campaigns.