I know you can hurt your fellow adventurers:
you can drop a fireball right on top of them
you can hit them with a splash weapon.
you attack them directly(hopefully because your confused)
What I am concerned with are the times when you believably could hurt a companion but where the rules are vague or non-existent.
For instance:
If your ally gets sucked into a whirlwind does attacking the air elemental endanger your ally?
Can you attack someone grappling your ally without risking accidentally hitting your ally?
Il you make a melee attack against a creature grappling your ally, you can't hit your ally. But if you make a ranged attack against a creature grappling an ally, you have 50% chance to hit your ally.
In 3.5, there was a special rule about bullrushing a creature. If you successfully bulrushed a creature, anyone could do AoO agaisnt the bullrusher (or the bullrushed). There was a 25% chance that the AoO hit the wrong target. I don't know if it's still the same in Pathfinder.
Il you make a melee attack against a creature grappling your ally, you can't hit your ally. But if you make a ranged attack against a creature grappling an ally, you have 50% chance to hit your ally.
The rule you are quoting was present in 3.5, but in Pathfinder there is no mention to the '50% chance to hit a grappling ally with a ranged weapon'. This because while in 3.5 the grappling creatures both shared the same space, in Pathfinder they are merely forced to be in adjacent open space.
In 3.5, there was a special rule about bullrushing a creature. If you successfully bulrushed a creature, anyone could do AoO agaisnt the bullrusher (or the bullrushed). There was a 25% chance that the AoO hit the wrong target. I don't know if it's still the same in Pathfinder.
About Bull Rush, the rules says that 'an enemy being moved by a Bull Rush doen not provoke an attack of opportunity because of the movement unless you possess the greater Bull Rush feat', so this is more clear cut; since the Greater Bull Rush feat does not mention the risk of being hit by the AoO of allies, it is safe to assume that the 25% of being hit has been removed, too (also, it would be extremely lame to take 2 feats only to have the chance to be accidentally smitten by your allies ;) ).
Just my 2c.