Bug with IgnoreConstraintNames and WITH NOCHECK constraints
If you specify IgnoreConstraintNames and two constraints have different WITH NOCHECK attributes set, then SQL Compare will try to create the constraint without dropping it first.
I was able to reproduce this issue on a database created from scratch with just two tables in it. Here are some images that illustrate the issue:
I also have a backup of both databases if you have any problems reproducing this.