If Facebook puts your tracking link on the ad instead of the offer URL, does it usually affect ad CTR in a bad way?
Also, why does Facebook do this and how can I prevent it?
Well, not sure - is the user influenced by the domain they see under the ad? Probably. Is it worth worrying about? Not really.
As long as you have proper redirection in place the ad will show the final destination domain, not your tracking link domain.
What you may see in the ad preview is not always what real users see.