Aircraft 'time in service' has never been and never will be the same as the time recorded as time in command of the pilots of that aircraft.
Without going into the tedious detail and exceptions, the general rules are:
- aircraft time in service is measured from wheels off to wheels on
- pilot time in command/dual is measured chock to chock.
Accordingly, pilots can and should be recording more time in their logbooks for a flight than the 'time in service' recorded for the aircraft for that flight. The pilot is in command/dual for a longer period of time than just the period from wheels off to wheels on.
If some FOI reckons the numbers should match, the FOI is an arseclown.