Lost words in Word Count

I just finished a massive writing spree and come to find that my tracker in Scrivener is missing 400 words. I know this is I keep track of my total words I write in an excel spreadsheet. Until today, both my total words counts matched each other. Now they are off by 400 words. No, I did not make an error in recording the words to the spreadsheet. This is not the first time it has happened. Every year for NaNoWriMo, my wordcount on my spreadsheet and Scrivener are different. I thought it was something I was doing. I know for a fact it is not me. It has to be Scrivener.

The only thing I can think of is I did compile it because I wanted to see why when I selected a group of sheets, the total paperback page were only 3 pages when the total pages printed was 35. This is only thing I can think that caused the error.