But when I breed it says they don't like each other?!
That's fine as long as he doesn't say "They prefer to play with other Pokemon than with each other." Them not liking each other just means it's a lower chance that an egg will appear.
By the way does the female have to be the one with the move? Or the male?
The male is the one who passes down moves and the female determines what comes out of the egg.
You're doing nothing wrong if Dodrio is male and Skarmory is female. Best of luck in breeding it will just take time :P