Repairing a roof leak is not always difficult. Sometimes just knowing exactly where to put the roofing cement is half of it. This video walks through repairing a roof leak if protruding nails are the problem. This is 3 different situations with the same general theme. All three nails are in different locations.
This is a common roof leak that is very easy to repair, especially on asphalt shingles. Over time the nails will work themselves up and will need to be repaired.