Can something stop me from becoming a Canadian citizen even if I meet the residence rule?

Meeting the physical-presence requirement is not enough on its own. An application will not be approved if you are under a prohibition. Most prohibitions are for criminal and security reasons, whether the matter arose inside or outside Canada -- for example certain offences, ongoing charges, time in prison or on probation, or a past revocation of citizenship. Such situations can make you ineligible for a defined period. You must also still be a permanent resident in good standing, with no unresolved issues affecting your PR status.