A vaccine is a preparation containing antigenic material and may be:
Whole live micro organisms,
Dead organisms,
Harmless version,
Harmless form of a toxin,
Preparation of surface antigens.

Vaccines can be given orally or injected.

Problems with vaccines are as follows:

Vaccines are most effective if they are live and mimic infection. Dead organisms are less effective.

Less effective vaccines may need booster injections to stimulate secondary response.

People with defective immune systems do not respond well to vaccines - don't develop good B and T cells.

People with protein malnutrition don't have enough protein to make antibodies or clones of lymphocytes and so don't respond well.

Live virus may pass out in faeces and infect others (use herd immunity to solve this - vaccinate large numbers at the same time)

Viruses / pathogens which regularly mutate and produce different antigens cannot be contained by vaccines e.g. flu. Minor changes (antigen drift) is fine, but major changes (antigen shift) make previous vaccines ineffective.

Certain pathogens e.g. protozoa have 100s or 1000s of antigens on cell surfaces. E.g. pathogen causing sleeping sickness. It changes its antigens every 4/5 days and so immune system can't respond. Plasmodium (malaria) passes through 3 stages in its life cycle. Each stage has its own antigens therefore vaccines would be needed with antigens for all 3 stages or be specific to infective stage (short period of time between mosquito bite and liver cell infection).

Antigenic concealment - pathogens evade attack by immune system by living inside cells e.g. parasiting T cells and macrophages, or live beyond the reach of antibodies e.g. cholera remains in intestine or conceal themselves by covering their body in host proteins e.g. some worms.