I just noticed even more issues with my account - I forgot I actually only redeemed 75,000 points + 2 certificates for my stay, so when I was refunded 40,000 points I was actually due 65,000 points.
Similarly, I'm staying at a second hotel for a week and used a week certificate which is no longer showing as attached (says my redemption is now 150,000 points + taxes/fees) and the certificate isn't even in my account. So when I login it states I don't have enough points for the stay which leads me to believe it swapped over to a points stay.
What a mess.