This is almost certainly a leak. You can still walk on the "spire" because you're colliding with the blockbullets brushes, not the prop itself. In addition, you mention the "paint geometry tool" which means you created displacements, and those do not seal a map (unlike the world brushes you created them from). If this is the case, you need to add more world brushes under the displacements to seal the hole they created.