If your enemy walks thru its own allies square, and that same square is in your threatened range, is that an attack of opportunity?
Yes. Being next to Ally squares does not change how they provoke attacks.
However, if that Ally has the Bodyguard feat (and is adjacent or within melee reach of the target that provokes the attack, and is adjacent to you), they may Aid Another as an Immediate Action (consuming an Attack of Opportunity they would normally get for the round) to Aid their AC.
Again, while it does not change how the attack provokes (unlike some effects, such as the Grace spell, or using Acrobatics checks to move at half speed to avoid provoking your attack), it does make the attack that it provokes less effective, and is something the opportune attacker should watch for. :)
