I dunno about this one....
There's a bit of misinterpretation going on about the disclaimer in the screenshot - that's primarily there because special offers can be for retroactive discounts applied weeks after the full listing fees were charged. The bit about listing start times is odd to me, because scheduled listing times are to the second when you schedule at a future date, and that's decided at the listing set-up stage, so there is zero reason eBay can't calculate at the point of submission whether a listing is scheduled to start at a date and time where 0 insertion fees apply, however I suppose one might theoretically go through the motions to do bulk re-listings before the clock ticks over into a new month, but not submit until after - that would be the only scenario I can see where "start time" results in listing fees being an inaccurate estimate.
Also, this is a problem exclusive to the bulk relisting tool, as far as I know - set up a single listing using the normal submission process, the estimate is 100% accurate upon the basis of submitting the listing there and then. However I have used the bulk relist tool (and even the bulk revision option) when I knew for certain the listings and edits should be free, but the estimate showed a cost. Once they were submitted, no fees were applied (and you can be assured I didn't attempt to pay the fees they initially calculated upon submission 
Plus, if they actually had been, I would have disputed it because I knew what my free entitlements actually were).
Which brings me to the flip side of my pondering "hmmm..."
That is to say, you actually seem fully aware of what the free listing entitlements are, and how many of those you use each month - in a courtroom (if you indeed took it that far), a competent defense lawyer for eBay would likely be able to see that, and wonder if you were not submitting the listings knowing full well the 40 free had been used, particularly if you had done this one more than one occasion (you say it's happened twice in your OP, but then subsequently say you have "several examples"), plus the claim of it costing you $40 so far would suggest similar, when your screenshot shows a cost of $13.20 - i.e. doing it once completely unaware, maybe. Doing it multiple times, especially if over the course of a couple of listing cycles, one could plausibly suggest it was a deliberate attempt to get extra listings for free (and to be clear, I'm not saying that's what you did, just that it could be argued as possible, and while it wouldn't excuse eBay of wrongdoing if a court determined that was the case, it has the potential to undermine your case).
Disclaimer: Not a lawyer
