yes and no 
not in the save file (as i know) but in the entity files of the planets.
each planet entity files has a list of bonuses that allways found (eg. pirate treasure at the pirate base)
and a list of random bonuses.
this list contains both types of bonues the positive ones and the negative ones, so you can decide if you want to leave
the good or the bad ones in.
but in all my games i had most times only one or no bonus per planet.
maybe if the bonus chance is increased this happens more often.