Depending on specie, plants may or may not lose water at night. However, even in those specie that this nocturnal loss occurs, the rate of loss is never as high as the rate of loss during daytime hours.
If you are losing water with the pumps turned off, then you definitely have a leak somewhere in the basin liner. he only way to determine the location of this leak is to leave all of the pumps off and let the water level drop till it stabilizes. At this water level, or slightly above, is where you will find the leak.
Any plumbing/piping that feeds water into the pond basin whose outlet is below water level must be raised above water level when the pimps are turned off, otherwise siphoning may occur.