From Quake Wiki

When you run QBSP on your map file and it leaks for whatever reason QBSP generates a file called a point file which is the name of the map with the file extension ".pts" in the same folder your map file is in. This file can aid you in finding the leak(s) within your maps. Open your leaking map into your map editor of choice. For example open the map in TrenchBroom then go to file menu, load point file..., load that .pts file and you will see a line shooting through your map pointing to where QBSP saw a leak.