The output of both flight crew and the css checker can be hard to understand. They do give you a line number where the problem occurred. Often the best thing is to just go to where it says it is a problem and take a look at it and perhaps compare it to an example in a working epub or to one at www.w3schools.com
One thing that is very annoying about the cleaning function is that it reports that there is an unmatched paragraph tag when in fact there is an unmatched tag of another sort, often an anchor tag, in the middle of a paragraph. That is after taking you far away from the actual scene of the crime.
If you do anything that is likely to result in cleaning, like switching views, etc, it is worthwhile to remember the line number so you can return to where the problem probably is.