It seems like you stumbled upon a different bug in HARP. We will try to fix this soon.
In the mean time you can work around this by excluding the lat/lon weight variables after you performed a bin() operation.
So, wherever you now use:
-ap 'bin(); squash(time, (latitude,longitude))'
you should use:
-ap 'bin(); squash(time, (latitude,longitude)); exclude(latitude_bounds_weight,longitude_bounds_weight,latitude_weight,longitude_weight)'