In v3.5.4 and v3.5.6, I'm running into problems with unexpected constraints being added when I copy an InnoDB database. If I don't check the "Add Constraints" box, the constraints are still added in the copy. If I do check the "Add Constraints" box, duplicates of the constraints are added. Through a couple copies in testing, I ended up with 8 copies of the same constraint.
Bug 3417 appears to be the same issue. It was supposed to have been fixed in v3.5.0 but it looks like the problem is back.