What happens if you go through your points history for the year and manually count your stays? Does clicking on something like past stays give a list going back through the entire year? Can you use credit card records to count stays or do you have all receipts collected together? What about email records of your final bills from each property?

I would start by trying to count stays very carefully. You might need to gather documents to send to SPG if they don't agree quickly that they have made a mistake.

I remember a few stories from previous years of folks having accounts audited where some incorrect night and/or stay credits were discovered.