What both guys above say is correct, but to give you a more thorough method of fixing it:
- In Visgroups, turn off everything but world geometry. That means turning off props, func_details, lights, etc. Basically anything that will obscure your view of the map, and that does not seal a room.
- Run map using Normal BSP, no VIS and no RAD. Make sure Do not run map in game is checked (you do not want TF2 to launch)
- Click Map, Load Pointfile (about halfway down the menu)
- A red line should appear if you have a leak. With areaportals this line will show you how the two faces of an areaportal are connected/touching. Start at one side of the areaportal and follow the red line all the way until you see where the leak is (usually two brushes not fully touching, or a previously func_detailed brush.
- Seal the leak, the repeat steps 2-4 until no Pointfile can be loaded.
Congratulations, you've fixed your leaks!
A couple things to note, first, use the SKIP texture on all of the faces that are not being used as Areaportals on an areaportal brush for maximum efficiency.
Also, don't forget to turn your Visgroups back on before doing a more thorough compile!