"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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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.
At the end, when Peter saves Mary Jane from the collapsing structure, he jumps up in the air and swings her to safety. However if you look at the web he is holding onto it is hanging down vertically. What did he attach the web to that was directly above him, the sky? Every bit of the structure around him was/had collapsed and the only thing remotely close to swing from was the cranes. Yet we see that was quite a distance away, so Peter would have had to shoot the web away from himself not above him.