Other mistake: At the beginning of the final fight between Johns and Riddick, you can hear actress Radha Mitchell's accent slip back to a Australian when she tell the group "leave the stuff, let's move...let's go". (01:17:30)
Other mistake: When Fry is looking around for Riddick at the end, she's holding the blue bottle of bugs to light her way. The blue light on her face isn't from the bottle as she holds it, as she's circling around in some cases with the bottle completely behind her, yet her face is still lit up blue.
Answer: The alien did it. Riddick is just starting to change a little bit, but he is pretty upset by her death nonetheless.
Grumpy Scot