I think I know the reason of both the things you have said are being left in mystery. Dharma corporation recruited one person to push the button so that planes don't crash and other stuff. So they were dropping food for that person survival. As for Boat shootout(if I get it right, what you are saying), I think they mentioned that they were 'others' and they didn't wanted to anyone leave the island so there were guarding the island so when some of the heroes tried to getaway they did a shootout to prove that no one can get away without their permission.
I think the biggest mystery was parallel timeline and the reason why they were there. I know that Jacob chose them cause they had no life but still some things are still not clear like what will happen to them(those who left the island in Azera plane) and what was all that leaving stuff the people of parallel space were talking about. Were they going to the island? And how was Jack's dad alive? Seriously, I was expecting more.
But to rate it, I will give it 9/10 cause it was nice finale after all.