Five usual sources, ordered by how strongly Fort Collins's own weather and housing record points at each.
Flashing and seams
Water follows the metal around chimneys, vents, skylights and wall joints before it ever reaches a shingle. A stain that sits right under one of those points to the flashing or its sealant.
In Fort Collins: Fort Collins has about 132 freeze-thaw days a year, the expand-and-shrink cycle that pulls those joints apart. That is #3 of 209 cities we cover.
Hail bruises that open later
A hailstone can crack the mat under the granules without a visible hole. The roof sheds water for a while, then leaks weeks or months afterwards, often in the first hard rain of the next season.
In Fort Collins: Hail of 1 inch or larger fell on 53 days in the county's NOAA record; the largest stone was 2.5 inches. That is #17 of 209 cities we cover.
An old roof wearing through
Shingles go brittle, sealant dries out and a second layer hides the real condition of the deck. When leaks appear in several rooms, the roof may be at the end of its life, not just one spot.
In Fort Collins: 31.1% of homes here were built before 1980 and the median home dates from 1992. That is #179 of 209 cities we cover.
Heavy rain finding a weak spot
Exposed nail heads, a worn pipe boot or a low-slope section only fail when a lot of water arrives at once. If the leak shows only in downpours, look there first.
In Fort Collins: 0.5 days a year bring an inch or more of rain here, out of 17.4 inches in total. That is #195 of 209 cities we cover.
Lifted or missing shingles
Wind folds a shingle back and breaks its seal; the next rain goes under it. From the ground you may see a bare strip, a flapping tab, or granules and tabs in the yard after a blow.
In Fort Collins: NOAA logged 14 days with 58 mph or stronger thunderstorm wind in the county since 2014, and a peak gust of 81 mph. That is #196 of 209 cities we cover.