Assumptions/Unknowns
1. The Black Hole and Unknown Event: There is no certainty that it was a black hole in the first place. The visual record on the ship was only viewed by the psychologist and the biologist. Also, the image of the ship traveling through time was the same as the image of the sphere traveling at the end of the film, but the sphere was not heading through a black hole. I would guess that the ship traveling back in time was either caused directly by the sphere or by a manifestation of a crew member, especially as there is no chance that a black hole would send the ship back in time directly to the earth and able to crash intact. The last member of the crew who had survived killing each other could have wanted to go back home, perhaps even wanted to go back to a time before they had found the sphere, and was only semi-successful in manifesting their desire.
2. The Foot Prints and the Opening Door: We never know whose footprints are in the dust. We also never know how they opened the door. Even if the sphere opened the door, it certainly didn't put footprints in the ship for no reason. Could someone have already gone in and forgotten about it? Could someone have still been alive on the ship? I have no idea.
3. At the Bottom of the Ocean: Would that ship have sunk if it never took on water? I don't know. Also, the body being in the chair on the ship holding a pack of almonds indicated that he sat down after the possible crash and, surviving any crash, he was also killed after the fact, indicating that someone else survived as well. I like to think that perhaps the ship was manifested directly to the bottom of the ocean and in the past by this man in an effort to prevent the sphere from even being found. Perhaps he was the only survivor and manifested his own murder. Who knows? :P I have no idea, but there are more possiblities than there are explanations.
I think there are more unknowns, but not all important. Like when the ship was from. Why they never found any more bodies on the ship (I know they didn't search much, but it's still strange, especially on a ship with trash cans that indicated there would be a decently large crew).
Anyone have any ideas that clarify anything here?