Three explanations, told apart by different tests
The first is anatomy that was never treated. Root canal systems branch and some canals are genuinely difficult to find, and a canal that was never located was never disinfected, so the bacteria in it were never disturbed. The second is reinfection from above: a restoration that leaked, a crack in a filling, decay at a margin, letting bacteria travel back down a system that had been cleaned. The third is a vertical root fracture, where the root itself has split along its length.
They are separated by different tests, not by one impression. A missed canal usually shows on angled or three-dimensional imaging. Coronal leakage shows as decay or a defective margin around a restoration that has been in place a long time. A vertical fracture characteristically produces a narrow, isolated deep pocket on one aspect of an otherwise healthy periodontium, which is why the probe is run right around the tooth rather than at the site that hurts.