So i just beat the game but i think something weird happend during my game.  At the part when you have to go get the three items to get your suit to full capacity, the objective line was telling me to go to totally different locations from where the items were. Next thing i know i have beaten the game having not picked up the hookshot or the other two parts of the suit.  Was picking these up optional or did my game glitch or something?

They're optional.