I'm not sure if the title is clear. I'll try my best to explain this problem.
In Pathfinder, when an enemy moves out of a square within your melee reach, you can perform an Attack of Opportunity (AoO).
Similarly, in Rogue Trader, you get a free attack (essentially an AoO) if the enemy you're engaged in melee with moves without making a Disengage action.
However, how would this happen if we could see the whole combat like a movie? According you RT's rules, every round lasts around 5 seconds (6 in PF I think) and everything happens more or less at the same time (not sure if that's also true in PF, but I think it is). How can you attack in one round but at the same time perform another attack? Is that like a reflex? I know not every action happens exactly at the same time, maybe one attack follows the other by a fraction of a second, but then if you have the ability to attack twice in a round, why don't you always do that?
Another problem i have related to AoO, is when you play a game that actually lacks AoO, like Rogue Trader:
In a fight, there was an NPC who moved very fast, ran a number of squares, passing next to a PC. My players argued that since the NPC moved into melee range, his character should be able to at least react to that and be able to do some sort of melee attack, however, the rules say nothing of AoO save from those who are engaged in melee. How do you explain that someone can't do anything about an enemy who runs right next to them? You could argue that it moved too fast for him to react, but at the same time, how can a PC try to dodge a bullet, or even have an AoO with the same NPC moving at the same speed, only because they were engaged in melee?
I know there's no perfect system and no system is ever 100% true to reality, but I'm just having a hard time imagining combat as a flowing narration. Bear in mind my knowledge of PF is very basic, I'm only good at RT.