many years ago I got dragged into the rubber gloves room becuase my passport looked like it had been slept with for 10 years (i carried around in back pocket without a cover) but the supervisor was fine with it, Interesting issue that arisen now, but Indonesia has always been well known to be suspicious of anything that is not in pristine condition, and its not just passports and money.
IMO this is embedded deep into the culture and I am not sure why, but they do try to keep anything in an As New condition. Its amusing to see household appliances still covered in manufacturers stickers, that everyone else would rip off as soon as we open the box, or leather car seats still covered in plastic. In my house I have 10 yo dining chairs that stilll have the manufactuers plastic over the cushion