There are a few leaks such as a location in Mine Copy. A example of a potentially big leak is fighter which leaks 2 locations and a rect (GUI region) every time the main action path runs. There are potentially others, with any leak that occurs frequently potentially helping towards poor late game performance.
GUI Replace Unit is used which leaks handle indices due to a game bug. Would have to be used thousands of times to make a difference though...
I would also suggest temporarily removing the Stealth System in case there are leaks or efficiency problems with it.