One small difference I've noticed when I was tabulating EQMs in my spreadsheet, is that the # of miles listed under "Flight details" in the mobile app for a reservation/flight is different from the number of EQMs/base RDM actually used in the calculation. Some examples (matching upcoming fights in the app against previous earning details in my account summary):
SFO - BOS:
Flight details distance: 2697
Earned EQM: 2704
SJC - JFK:
Flight details distance: 2561
Earned EQM: 2569
SFO - JFK:
Flight details distance: 2579
Earned EQM: 2586