There are numerous threads reporting this, but I'm too lazy to look right now, so I'll repeat my rant here...
This is a known issue with MR, and has been for at least two years. If you catch it and call Marriott, they will correct the booking and only pull the points that were being charged at the time you booked.
But...
Although they claim their system will automatically catch and correct this, they've had two years plus to take care of this, but they don't. One cannot help but believe that they are intentionally pulling the additional points, hoping that guests do not notice or think they have to pay the higher points. It is very anti-consumer. It's slimy. It's wrong to continue to do business this way. How many points are being taken this way? How much obligation do they take off their balance sheet through this deceptive practice?
OP, you are right to have a bad feeling about Marriott because of this. I am usually understanding of what Marriott does, but in this case, it seems they are trying to be deceptive and have no interest on correcting the issue.
End of rant...
OP, one more thing... Go to the Marriott Rewards Insiders site and post your valid concern there, too. Marriott pays more attention to what's posted there than what's on FT.