Why a roof vent boot can leak
The pipe through the roof is an interruption in the shingle surface. A small split beside that pipe can admit water while the shingles around it still have useful life.
The collar and the flashing have different jobs
A plumbing vent boot includes a flashing base integrated into the roof covering and a collar or other seal around the pipe. The base directs water back over the roof. The collar closes the space at the pipe. A split in that collar leaves an opening at a raised point in the roof.
Rain entering there can follow the pipe or decking before it reaches a ceiling. The indoor drip can appear away from the original opening. Looking only at the shingle directly above the stain can leave the failed boot untouched.
A boot repair needs sound surroundings
The useful repair begins with the whole detail: collar, base, fasteners and the adjoining shingle courses. A specified repair part can suit one condition; another roof needs the boot replaced with surrounding work. The choice depends on the actual component and how it can be integrated.
The neighboring shingles must be workable, the replacement compatible and the connection to the deck and water-shedding layers sound. Brittle covering or deteriorated support can make the work larger than the visible split.
Roof leak repair
Why surface sealant can miss the repair
Sealant has a role in specified roofing details. Smearing it over an old collar does not replace missing or broken material underneath. Movement around the pipe and weathered surrounding surfaces can also keep a surface patch from becoming a reliable connection.
A repair needs to address the component that failed and restore how the detail sheds water. That is a different task from hiding the gap from view.
A local problem does not automatically mean a new roof
A failed vent boot can be a local defect on a serviceable roof. The question is whether the repair can tie into sound adjoining material. If the covering is brittle across the slope or earlier repairs have compromised the surrounding detail, a larger scope deserves discussion.
Tell us about the room with the leak and roughly when you noticed it. There is no need to climb the roof or identify the failed part before requesting help.