There was an exhaust vent that was installed broken. It appears as if the vent had been sitting and the plastic had deteriorated and turned brittle and when nails were put in it the flashing cracked and allowing in water. Removed this vent and installed a new 4 inch black exhaust vent. Sealed the flashing on a 3 inch exhaust pipe flashing that was allowing in water. Also, beside these two spots was a chimney that was allowing in a bit of water – sealed the flashing and where the shingles meet the flashing. Sealed the chimney flashing on opposite side of roof as well. Rest of roof is in good condition and was installed with good underlayment.