If you notice a course that has a red exclamation point next to it in your audit, that means you have taken the course, but it's not counting for that requirement.
There are a couple quick things to check to see why the course isn't counting:
The course has no units/credits/points or no grade awarded
The course was failed, withdrawn, incomplete, or otherwise doesn't meet the minimum grade requirement
The course was taken P/F (as a default, 'passed' courses don't count, but the audit will allow it if a P/F constraint is added to the requirement)
The requirement has already been satisfied with a different course, or courses.
The next thing to check is if the course meets all of the constraints (rules) of the requirement you expected it to satisfy. You can check on the constraints by clicking the constraints button next to the title of the requirement.
It's also possible that the same course is already counting for a different requirement in your audit, and double-counting is not allowed. You can check this by searching (using command+F) the course code on your Progress tab.
You can also click on the course to pull up the course info sidebar. It's possible the course has an equivalent or anti-requisite that is also in your record. In that case, this course won't be able to count.