Most flat top roofs are made up of layers of asphalt, roofing paper, asphalt, roofing paper, asphalt, roofing paper, and then gravel. Although most leaks are caused by damaged or poor flashings, the built up membrane itself can get old and worn.
The gravel serves to keep the UV rays of the sun away from the asphalt. So the first areas of damage are those where the wind or the snow has swept away the gravel. For good maintenance you should be up on the roof once a year making sure that all the asphalt is covered by gravel.
Once the sun can get to the asphalt it will dry and crack, exposing the roofing felt. And that is how the sun works it way through the two or three layers of roofing until finally the roof itself leaks.
Small problem areas can be patched by clearing off all the gravel, opening the bubble, then closing it flat with fresh asphalt. Professionals will use a propane torch to melt the fresh asphalt. DIY'ers will use a "cold patch asphalt" (you don't really want to work on your roof with a torch). Then you put a new patching membrane, then more asphalt, then a wider membrane, then more asphalt and finally cover it all with gravel. You can do even smaller patches with a "fibrated asphalt patching compound" that has fibers in it to accomplish the same things as the membrane (almost). Just putting a patching compound without fibers, and not protecting it from the sun, will last only a few months. Aluminum paint can be used to cover any bare spots but especially on flashing patches, to keep the UV rays away from the asphalt.
Trevor Stevens from Norman & Collie in Montreal was the roofing expert who walked us through this inspection and did the patching with IKO products.