You would think the bit in Riddick's mouth is there to keep him from biting people. Take a moment and you'll realize it's so he won't talk to anyone because his mouth's just as dangerous as the rest of him. He's dangerously charming, and the children especially seem interested.
Johns shoots morphine into his eye socket, instead of putting it in his arm like one would expect. Combined with the implication that he stole the morphine from the ship's medical supplies, it becomes clear that he is doing this to avoid leaving visible needle marks on his skin.
The morphine was actually his own stash, as they are hidden a box of fake shotgun shells. However, as pointed out by the director of the film in the scene where the group finds Owen alive but critically hurt, when Carolyn is informed the back of the room where the medkit used to be is gone, Johns has a look on his face that is clear that he knows he could make Owen's last moments painless but choses not to for his own addiction.
At some point in Pitch Black, the creatures turn on each other and become cannibalistic. Well, considering they have to wait 22 years just to ''feed'...
Either that, or they're fighting over mates and have to wait 22 years to do something else that starts with "F".
The raptors don't come out during the Eclipse just to breed - they can do that underground just fine. They come out during the Eclipse because they can. It's then that they really have room to get killing and eating each other above ground, which thins out the weak and old, and results in all the skeletons. It's been going on for hundreds of thousands of years. And this 23-year cycle is what prevents any sun-based life from evolving.
Before they head to the skiff, Riddick warned about cuts because the Raptors now know about human blood. In a brief moment, Jack panics. At first, it looked like worry in general. However, upon second look, Jack is specifically worried because Jack's a girl and is bleeding.
When Johns gets up after the crash, he's disorientated. It could simply be because of the crash and the fact he wasn't in a good secure way to avoid any damage (He was out of his cryo-sleep bed and simply holding onto some furniture) or he is having his drug relapse, or both. Has to be both because of how the medicine cabinet was missing/empty.
When Zeke dies, Shazza quickly runs towards his location and screams his name. Riddick was actually there all along, they look at each other and during that, there's a brief shot of his "boneknife", which is devoid of blood. Either he really didn't kill him (which he of course didn't), or he was quick enough to clean his knife rather perfectly.
On the other hand, given it's Riddick, the other castaways have no reason to assume he'd only crafted one shiv. Not as exonerating from their POV, although a bit more so for the audience who already expect monsters at that point.
And as pointed out, with the amount of blood found in the hole, Riddick would have been covered in it if he had been the one who committed the act. However, like the shiv he had on him, he's bone dry of blood.
Edging into Fridge Horror: The cries of the creatures! The crooning calls sound non-threatening, but the creatures are anything but. The crooning are either the sound of their echo-location, or just the noise they make to each other. On the other hand, it could be both: for a creature that lives and hunts in darkness, why not evolve to sound non-threatening to lure disoriented prey to you because you sound safe?!
The only other living organisms that the castaways encounter besides the Bioraptors are little wormy things that glow in the dark. Considering the Bioraptors' main weakness, bioluminescence would be the equivalent defense mechanism against them to an Earth species being poisonous to touch.
The first proof of a previous human presence on the planet which the crash survivors find? It's a toy. Not a tool or a container or some other piece of practical equipment, but a toy. The geologists who'd lived and horribly died there 22 years ago had at least one child with them.
Riddick finding the spectacles just outside the chained-shut door gets creepier when you know what happened to the geologists. Whoever wore those glasses was probably eaten alive there, perhaps while begging whomever sealed the doors to open up and let them in.
