Antigenic differences between the vaccine and challenge virus eg equine influenza.

Increase in virulence of the challenge virus e.g. IBDV and Mareks disease.

Break down of the cold-chain during during transport e.g. tissue-culture rinderpest.

Improper administration- disinfectant in the syringe (or water supply to the chickens- use 5% skimmed milk to neutralise free chlorine).

The vaccine has been overgrown by an irrelevant virus/bacterium, no antigen-potency testing done.

The vaccine has fulfilled safety criteria for its license but has never been shown to work when challenged, more common than you would imagine (see Outbreak of canine distemper in vaccinated dogs in Finland by Ek-Kommonen et al., Vet Rec, Oct 1997, 141, pp380-3).

The vaccine is homeopathic, you might as well con the client by injecting coloured water.