I would check with the author of CMX as to whether the add-on shows those stacks even if they’re not implemented by the game.

Since FoN’s pen doesn’t show up on your character sheet, as it’s effectively a debuff on the enemy, the add-on may be seeing you have FoN slotted and looking only at the number of status effects on the enemy to report stacks, regardless of whether the pen is applied.

You could theoretically also do the math yourself using your logs to see if the extra pen is applying, but with so many variables constantly shifting in BGs that could be difficult.