Why flat roofs leak
Water does not run off a flat roof fast. It sits, finds the weakest seam and goes in. Roll roofing and older built-up roofs crack in the heat. Coatings wear thin and need a new coat every several years.
Repair or re-cover
Small blisters and open seams can be repaired. If the roof is soft underfoot or ponds across most of the surface, it needs a new membrane and sometimes new slope built in. Your estimate will show both options if both are possible.