You make some good points, it is possible my logic is entirely wrong.

What I'm trying to count under the "Excused Exceptions" heading is the following:

1) Where Late clock ins are less than 15 mins (0.25 in decimal time) and do not equal zero
2) Where Early clock outs are less than 15 mins (0.25 in decimal time) and do not equal zero
3) Where Shift column (column E) contains the word "Flex" AND the corresponding row in column L is "Unmatched target"
4) Where worked hours (col J) is greater than target hours (col I)
5) Where Swap (col F) is equal to "Y" AND column L DOES NOT equal "Missed a clocking" or DOES NOT equal "Swiped outside of shift & Missed a clocking & Unmatched target" or DOES NOT equal "Swiped outside of shift & Missed a clocking" or DOES NOT equal "Missed a clocking & Unmatched target"

These are the explanations of the countifs I currently have. The problem, as you can imagine, is that a count in 1) might also be counted in 4) for example. Do you have any idea how this could be avoided?

Or, indeed, if there is a better way of doing it that I am not thinking of? All help appreciated. It is entirely possible my brain is fried thinking about this too much and I am off track!