Just so no one makes the same mistake I did, on my second playthrough I sequence broke and got the missiles early. I had intended to 100% this run but getting the missiles early made it impossible to pick up the first missile pack you are supposed to get, as the cutscene would not trigger.
 
Apart from the bugs and a few other minor issues, I am loving this game.

Thanks for the heads up. How do I know if I get them early or not?

It would be very unlikely to get anything early without realizing it, you have to go out of your way to do so. Apart from that, there will be a cutscene if you pick up the missiles at the proper time/place.