"The Punisher" has a small cameo in Spider-Man 2. At the end when Mary Jane is running through the park with her wedding dress on, Thomas Jane can be seen glancing at her while she runs past. [This cameo has been highly debated for the fact that Jane is not credited. While uncredited cameos are not unusual, there does not appear to be any reliable source that confirms or denies his cameo in the film.] See more...
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Plot hole: Harry tells Doc Ock that in order to find Spider-Man he must find Peter first. Doc Ock finds Peter with Mary Jane in the cafe and throws a car through the window straight at them, then later throws him against a brick wall. Any normal man would've been killed instantly, and Doc Ock doesn't yet know that Peter is Spider-Man. Given that Peter is his only lead on Spider-Man, it makes no sense that Doc Ock would effectively try to kill him.
Factual error: Considering the brightness of the fusion process, Dr. Octavius has to wear special goggles to be able to see it. Yet no one else in the room is wearing such goggles or seem hurt by watching the whole process, just as at the end of the movie. When welding something, no one can look at the arc that's created, as it would hurt his eyes and burn his retina; presumably, the fusion process would be brighter and more powerful than that, and so should have some kind of damaging effect on everyone's eyesight (except Spider Man's, maybe).
Factual error: Dr. Octavius says his fusion relies on tritium and that there is only 25 pounds of the substance in the world. In reality, tritium is a good deal more common than that. From this article (http://www.epa.gov/radiation/radionuclides/tritium.htm): "It is used in various self-luminescent devices, such as exit signs in buildings, aircraft dials, gauges, luminous paints, and wristwatches. Tritium is also used in life science research, and in studies investigating the safety of potential new drugs." There's also a large region of water near Antarctica which is rich in tritium.