This seems to happen to any BSP geometry that are directly touching and share similar dimensions, as I’m having the same issue when attempting to use separate BSP brushes to use different materials; once I build the level, the brushes seem to all merge, and I cannot select single brushes within the mass until the “selection” is moved. In this example, all BSP geometry has the same height and width, 100 units, but varying length, yet they all still merge once the map is built:
Once the mass is moved, they all revert to being separate geometry pieces, but the problem will return once the map is built again, so I am stuck with either having unbuilt lighting, or corrupted geometry causing texturing issues.