Earlier quoted context omitted.
If they refund the entirety of the second transaction, logic follows a third transaction of $9,975 would be correct if you actually wanted to buy $10k. I suspect that's not what's going to happen though. OP will get a refund of $25 + $9,975.
You're forgetting there appears to be a race condition at play. The third transaction was marked as canceled because the second has not finished processing and so is still counting against the total. There is no guarantee the govt system will check that again once 2 completes (in fact, I'd be shocked if it did). And by the time both 2 and 3 process, the window to buy looks like it will be closed per the author's post…
The order won’t actually matter here - but even if it did, the “right” thing will happen either way depending on which interpretation of the email you have.
The third transaction got the same response as the second. Which would actually imply that the common reading of that email (he’s getting $25 back from the second deposit is correct, and he’s going to get the entire $9,975 back from the third.)