Are the Draugr apologizing to me?
Draugr sometimes say "Unstaad Krosis" when attacking. I understand that means "many apologies" in dragon tongue (convo with Paarthurnax).
Does this hint that they are doing something against their wishes?
Solution 1:
[Not a complete answer, but too big to be a comment.]
Unslaad Krosis, literally means, "Eternal sorrow", according to UESP, and the lore page on draugr confirms that they do indeed say it.
However, the draugr were in life the servants of dragon priests, and upon their priest's death they would be entombed with him as his eternal servants and guardians; there appears to be nothing unwilling about it, and the lore article even specifically debunks the common Nord misconception that draugr are cursed. Draugr are, in fact, the undead servants and guardians of their immortal dragon priests.
This leads me to conclude that they are not, in fact, apologizing to the Dovahkiin as they attempt to disembowel him/her, especially alongside another common phrase listed in the aforementioned lore article, Daanik Ah Dov, or "Doomed dragonhunter", which appears to clearly be a threat.
I cannot, however, offer a clarification of the meaning of Unslaad Krosis in the context of the draugr mutterings, other than to offer my personal observation that dragon language appears to be at least somewhat idiomatic, and that oftentimes words seem to have deeper philosophical meanings than what a direct English translation would suggest.
Solution 2:
It actually means "Unending Sorrow." "Krosis" can mean both "sorry" (as Paarthurnax uses it) and "sorrow," apparently. Otherwise we'd have a Dragon Priest named "Sorry." It would seem like Paarthurnax's usage is less literal than elsewhere.
The word wall for the last word of Storm Call uses it thus:
Qethsegol vahrukiv sahsunaar
Do daniik vundeheim ag
Nahlaas naal qo do
Unslaad krosis(This) stone commemorates (the) villagers
of doomed Vundeheim, burned
alive by (the) Lightning of
Unending Sorrow.
As for draugr being held against their wishes, there's some lore on a researcher who managed to gain their trust and infiltrate them. They seem more fiercely territorial than anything.
Solution 3:
They are just being sarcastic....."Really sorry but im gonna have to kill you now"