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 Peter against a brick wall. Any normal person would've been killed instantly (or very badly injured), 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 try to kill him.
Plot hole: Dr Octo builds a new, bigger machine and it starts to pull the building in on itself, but it's so strong it also manages to pull all the metal from the streets as well, including cars. When Spiderman saves MJ, the metal cranes have somehow managed not to be pulled in or at least bent by this massive machine that made a building collapse on itself.