Yeah, this is a case where different mechanics or behaviors are being called similar things. Generally speaking, if someone tells you to "stack up" or something similar theyre saying for the group to all stand together. This is done for 2 types of mechanics(it also generally makes healing easier - also a plus). One type(the more common one), is where the next damage attack from the boss will be split among everyone hit(this is usually indicated by marking the targeted player with 4 arrows pointing inward toward them). If for instance the incoming attack is going to do 200k damage, that will likely kill any individual player(sometimes a tank can eat one of these attacks using an invulnerability skill and survive, sometimes they cant). But if the full 8 man party stands together that goes down to 25k each, which the healers can easily handle. The other type of mechanic where people try to stand together is the type where the boss is going to aim a very large aoe at every individual party member. If everyone is spread out, there might not be safe spots to stand - so standing together ensures that youll have somewhere to go.

The other "stack" is what Hysterior is describing from Aurum Vale. Two of those bosses have moves that put a poison on you that the healer cant cure. The more of the bosses moves hit you, the higher then "poison stack" gets. At 4 or 5 stacks it becomes almost impossible to heal someone through it. So you eat the fruits in the arena to cleanse the poison. But as Hysterior said, there arent enough of them to have one each time you get hit so ideally you wait until your poison stack is a little higher. This puts pressure on the healer, but not overwhelming pressure. It also means the DPS have to go fast enough to end both fights before the fruit completely run out.