Have noticed this as well. Normally I don't track MQDs very closely....that's a job for the accounting people! But as the year draws to a close, I looked at where I was at and what trips I had left to do, and, booked them more strategically than I otherwise would have, specifically to do with the cost of the fare. Flew and see rather large discrepancies. Like the OP it seems to have affected flights that got changed into more expensive fares, to my MQD detriment.

But it begs the question of how many other fares have been affected. I change flights all the time. I'm likely going to have to audit the whole year's flights against fare paid to see if there's other MQD missing. Just what I wanted to do...not.