My normal did that when I first got her. 3 of the first 4 meals were eaten in a...non-standard manner. Two she ate butt first. One from the very tip of the tail. Looked like some sort of weird spaghetti thing going on. One she tried eating from about three different places (rear left leg...middle of the body width-wise, etc). On all of them she took much longer to figure things out than the other snakes. She would sniff and sniff and sniff the body after she finished killing it for 15 minutes trying to find the head. She was either laying on it, or skipping over it, or it always seemed to be something. Then I think she got frustrated and just started eating wherever her head happened to be. It was simultaneously a bit frustrating and a bit amusing watching her.
She figured things out though. All meals go down head first now. Your's will figure it out, too.
Just out of curiosity, how big is the snake in question?