Adaptive Immunity - Limitations

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Adaptive immunity works great when lymphocytes identify pathogens and make antibodies to their antigens, activate cytotoxic T cells against the pathogen, and form a reserve of memory cells that can respond to future exposures. Unfortunately, sometimes things go awry!
1. Antigenic variation: pathogens such as Plasmodium (causes malaria) and influenza virus regularly switch out which antigens are on their surface. This means that the memory cells would not recognize the pathogen anymore.
2. Memory cells don't last forever. With repeated exposure, memory cells are stimulated to keep proliferating and to keep making antibodies to the pathogen. However, over time, and without repeated exposure, the memory cells will undergo apoptosis to make room in the blood and lymph tissues for memory cells that are more actively being stimulated and exposed to common pathogens. Thus, booster shots are employed for some diseases to stimulate the immune system to keep antibody levels high. A titer can be sampled from the blood to measure immune levels.
3. Cross-reaction of antibodies with "self" tissues. This is especially common when antibodies to the pathogen also match host's heart valves (Rheumatic Fever is an example of this), kidney cells (post-infection glomerulonephritis), and joints (post-infection reactive arthritis).