How can an aircraft owner/operator track unauthorized flights?
The owner could do regular checks of the aircraft's Hobbs meter, and if the times don't match what the log is saying, then there could be some red flags being thrown.  

If someone it out to deceive, I'm sure they could get around this, but maybe then, the problem is giving access of expensive equipment to people who aren't trustworthy.

There are GPS tracking systems that could keep a movement log in memory.