Listed below are some examples of: Poor workmanship, Improper roof flashings, Defective roofing material, and The neglected roof.

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Finding Roof Leaks - Flat Roofing
The Most common problem we see when inspecting low sloped roofing is the drains or scuppers. They are normally plugged and prevent water from draining off the roof normally. This not only causes backup in the roof drain area - It also causes water to back up everywhere else on the roof. The Next common problem we see is the flashings and seams are not sealed correctly or have holes in them. Check all roofing penetrations and roofing seams for cracks, holes, loose roofing material, or even excess tar where these areas have been patched previously. Maintenance companies HVAC, sign companies, lighting maintenance etc... These service repairmen also can cause problems not only by dropping tools on rubber membrane but moving equipment around on roofing materials. It is a good idea to keep track of who goes on your roof, when, and what was done these precautions can make finding a leak very simple We have roofing maintenance programs we set up for larger commercial buildings. We normally inspect and clean twice a year. This type of program can save thousands of dollars a year by extending the life of the roofing material. Stopping leaks before they cause thousands of dollars worth of interior damage.
Finding Roof Leaks Shingle Roofing - Steep Sloped Roofing
Poor Workmanship is the most common problem we see when inspecting shingle roofs. Pipe flashings, chimney flashings, wall flashings, All Flashings should have positive lap. Water should run off the flashing and onto the roofing. These detail areas are the most important part of your roofing system a lot of homeowners think anyone can put a shingle on. This is true in part but most leaks we find are not the shingles themselves they are the detail areas.  An experienced roofer will know how to install shingles as well as flashings correctly.
Condensation is also very common here in Minnesota. There are not many roofers that can diagnose this problem right off the bat. Some roofs we see have gallons of tar spread around every penetration. the homeowner themselves are at a loss cannot figure out why They have had so many roofers out and still cannot find the leak. Condensation usually happens on the coldest days below freezing.  Keep an eye on the area that seems to be leaking. If the Roof leaks only in the winter months and not necessarily every time it rains this is a good sign. Also if possible check the amount of insulation in the area and for proper ventilation.
Ice Dams are another common problem and are similar to that of condensation check the insulation and ventilation. If you have snow on your roof and it is well below  32 degrees you should have minimal snow melting off the roof. Look at some of your neighbors houses do they have snow on them long after the snow has melted on your roof?