When Hunt is Climbing Rocky Surface near the end of the movie just before he jumps down the drain he is wearing a pair of cream coloured cargo pants, but later on when he fighting Sean on the beach after the bike chase he is wearing Black Pants.
Yes, it's true that Hunt is wearing Khakis when he infiltrates the Biocyte storage facility on the island. However, remember that he changes outfits with Hugh (and faces) to confuse Sean in the end. He keeps Hugh's outfit (leather jacket, black t-shirt, and black pants) when he runs outside, and hence, he's still wearing black pants until the end scene on the beach.
Ok, um, how could you not pick up on the outfit change? That was like one of the coolest things about the movie. The whole outfit/face change thing. He beats the crap out of Hugh, switchs outfits/faces and then drags Hugh, looking like Tom, to Sean Ambrose. Sean shoots him and sees the bandage on his finger (ewww!) and knows he's been double crossed. And like, can no one remember what these peoples names are? The woman is Nya, Tom Cruise character is Ethan Hunt, the "main bad guy", as everyone is calling him is Sean Ambrose, and the really good looking blonde guy, who is really evil is Hugh. Can you people remember that?
It takes professional make-up artists hours to get those masks on and looking right, yet through out the movie they were able to get them on in seconds. How?
if you played the video game or i think the first one explained, the masks are done with a small machine that scans a face and makes a latex match and it only takes seconds, or long enough for the latex or whatever to dry.
Yea..and duh...one of these "small" machines that can scan in seconds and outputs a plastic mask must only way uhm, like 90 LBS !!..gee any secret agent could easily hide one and pull it out of his magic bag within seconds, scan the bad guy, put on the mask, and hair, and voice activator, and contact lenses, and height and weight changing apparatus...etc...etc...
Well how did Ethan Hunt get Hugh's face mask anyway? Was he planning to beat him up and take his place and have hugh take hunts place? how did he know to bring a mask of his face and hughs face???
One of the best things about the original "Mission: Impossible" television series was that, just as you thought the team had slipped up and been defeated, it turned out it was all part of their plan and they were still completely in control. So, yes, in that spirit, I believe Ethan had planned to switch identities and had both masks all ready to go.