Changing temperatures cause your roof to expand and contract which triggers movement in the roofing system. During movement the membranes rub against each other and crack.
Plastic/Rubber Boot crack
The sun's UV rays cause plastic/rubber to dry out and crack which results in a gap between the pipe and surrounding flashing. This gap allows water to get in between the layers that protect your roof.
Over time metal flashings will rust when exposed to the elements. Rust cannot be simply sealed over, as it will continue to grow.
A tight bond is formed when the modified roofing membrane seals to itself. Over time, nails may begin to protrude through the top surface of the membrane causing rust and seepage to get between layers.