It's not so much that Miyuki thinks Velvet apologized for self-preservation, as it is her believing Velvet did it to "save face".  Basically an act of making yourself look good by taking responsability, but not actually meaning or being sincere in your words, only doing it to "look good" . compounded by the fact that Velvet apologized in the cafeteria, during dinner time, when there's a ton of people around to see and hear. :P

Given that Velvet is so well-travelled and has been to Japan and can speak fluent japanese, you'd think she'd have [i]some[/i] idea of what japanese youkai are capable of doing to her... Unless she purposefully avoided any local monsters when she was visiting there and only hung out with and around humans... In whcih case... ... She an idjit? 8D

Also, Miyuki doesn't [i]only[/i] do curses. She's got plenty of just plain old magic spells. Like setting things on fire. Lots of fire.