brockenspectre,
As far as your first question, I cannot answer this as I am not an ATCO.
The second I can hopefully. If I ever find out that we are on an incorrect heading/course than that given I will always advise ATC of the cock up. Aswell as this I find it incredible that the Captain of this aircraft you were on didn't look up and confirm the change in altitude. I can only speak for myself and my airline but the SOPS ensure that there is always audible confirmation of altitude changes even if someone has been away talking to handling/getting weather etc.
Regards le loup garou