When they first reach the jungle, Rusell has to go to the bathroom and just does it there in the dirt. We never see him wash his hands after that, and then just right away he touches and eats the chocolate he gives to Kevin.
Uh, as someone who has gone camping, there are ways to do one's business without touching a lot of gross stuff. It's not that horrific. And we don't see Russel washing his hands for the entire trek. Not that he could, since there's no running water or soap. I'm sure he's touched worse things than some dirt and his own waste all while feeding bits of that chocolate bar to Kevin.
Maybe he's got a bottle of hand-sanitizer in his pack.
The pilot caps Muntz keeps as souvenirs of the "trespassers" he dealt with look identical to the one Carl owned as a child and he owned that cap because he was a fan of Muntz. In other words, young explorers came to Paradise Falls to see if they could find Muntz and his bird, and got killed by their childhood hero.
Along a similar line, one of the dogs had said "I like you temporarily." This takes on much darker tones when you realise how temporary that "like" could be... and that the dogs knew it, too, because it had happened before.
In the short "Dug's Special Mission" we find out Dug's birthday wish was for a new master. This begs the question: just what the hell did Muntz do to poor Dug that led him to make that wish?!
More then likely? Neglect. Muntz has a lot of dogs, and Dug most definitely isn't the favorite.
Here's a more darker theory: Dug's original owner was one of the explorers who was killed by Muntz.
When they fly back home, Carl and Rusell are wearing aviation hats. Cool eh? Wait.... where did they get the hats from? Yeah, sure take the dead people's hats Carl.
Maybe Muntz has spares/extras?
How did Russell get onto the porch? We never see him during takeoff, but he says he was underneath. It's established very early on that Russell is anything but athletic. So how'd he get up there?
Adreneline rush kicked in. People do crazy stuff when their lives are on the line.
How did Muntz get his hands on the Wilhelm scream sound clip? Wasn't that thing first used in the '50s?
Dobermans and Rottweilers make sensible guard dogs, and could probably be used for hunting if you trained them well. But English bulldogs, like the one that went along with Alpha and Beta to hunt down Kevin, are far from athletic enough for such jobs and would probably faint from overexertion if they attempted to perform them. Now, this could be overlooked if he were built more like the original bulldog breed (which was probably still around when Muntz went on his expedition), but he's clearly a modern bulldog. What the crap is he doing going hunting in the South American jungles?!
The Methods that the scientific community used to discredit Charles Muntz's Fossils have been themselves discredited over time as grossly inaccurate.
In the first few minutes when Russell is telling Carl about the Wilderness Explorer badges, he mentions that the ceremony for the promotion to Senior explorer involves all the dads attending. That's why he's so dedicated to getting all the badges: he wants to see his dad. This even makes the ending a bit heartbreaking: Russell's dad doesn't bother showing up to an event that specifically calls fathers to participate in. It's nice that Russell has Carl in his life at that point, but what a douchebag Russell's father must be!
The first or second time that you watch the movie, you wonder how Carl, obviously an older man, would have survived without running water, electricity, or an unlimited food supply. But then you realize that Carl never wanted to live in Paradise Falls. He wanted to die there.
At the end, Carl, Russell and Dug are playing a game in which they point out the colours of cars. Dug shouts "grey one!". At first, you think nothing of it. Then you realise: Dogs are colourblind.
Can a joke based on scientific inaccuracy be labeled as Brilliance? Dogs don't see in black and white, they're red-green colorblind. Dug would be able to see blue, yellow, and violet in addition to greys, white, and black.
Then it was a red one!
Dogs interpret red as yellow. It was more likely actually gray.