I looked at 2017 FDA paper that identified 22 cases of Phase 3 trials rejecting results of Phase 2 between 1999 and 2017. Out of these, 7 were vaccines, and only one of them, V710 against staph infections in hospitals, was rejected due to safety concerns, the rest due to low efficacy. It took 8,000 patients in Phase 3 to detect the issue. Not stated in the text, but it seems it did not take much time (complications followed vaccinations, not long term effect).
Caveat: authors are saying that not all negative results were published before 2008. After 2008, tests needs to be registered with clinincaltrials site before starting, so all results should be reported, including negstive.