iTunes Connect DAILY reports for our app shows lets say 52 purchases a day... but according to our server logs, there was 55 purchases processe
If you confirmed that there is no Refund. How about a Reversal of an accidental purchase (eg: purchase 2 times)?
If you read Appendix L - Newsstand Report Field Definitions for
https://www.apple.com/itunesnews/docs/AppStoreReportingInstructions.pdf
There is a field Sales/Return:
Can be S or R. R is a refund and not a reversal.
It is reasonable to believe that Apple treats Refund and Reversal differently. I believe that when it is a refund, you will see a negative value under Units on your daily report, but for a reversal, the entire transaction might be cancelled out and not even appear on the report.
I am unable to confirm on that with 100% confidence, I guess you may drop an email to Apple Itunes Connect Support for more info on reading the Sales and Trends and daily report.
Added a Screen shot for Reversal (Apple does not mention Refund):-
So is the Report By Apple treat Refund and Reversal different? You have to ask Apple support.
Add extra screen shot:-