Capturing the Friedmans (made by the same director as The Jinx) was originally going to be a short film about children's birthday party entertainers. While researching the film, the director discovered that one of his subjects had a past of child sexual abuse and completely changed the subject of his documentary to focus on this family. Kind of a similar situation, but not exactly.
Another interesting example is My Kid Could Paint That, a documentary about a child prodigy abstract artist. Halfway though making the film the art world started questioning whether the child actually painted the paintings attributed to her, or if her parents painted them. At this point, the documentary takes an abrupt shift and starts investigating the family and the daughter's painting abilities. The results of their investigation is inconclusive though, so I guess no new evidence was found in this case.
The Act of Killing is kind of build on the premise you are describing, but under different circumstances. The Cove is close to what you are looking for, the main difference being that the filmmakers made the film with the specific purpose of finding incriminating evidence for the crimes it was documenting.
There's also been cases of people being acquitted of crimes based on evidence discovered in movies. The Thin Blue Line is the most famous example, but other examples include Gimme Shelter (a killing was caught on camera, but the victim was shown to be holding a gun, which helped the defense prove self defense) and Curb Your Enthusiasm (the main suspect in a murder case claimed he was at Dodger stadium when the murder took place, but had no proof he was there. Curb Your Enthusiasm happened to be filming there that day and while the man did not make it into the episode, he was in deleted footage, proving his alibi and acquitting him of the murder charge).
Dear Zachary and Paradise Lost are two more close examples.
My film blog:
http://gabrielbruskoff.wordpress.com
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