Your map has a hole in it, called a leak. Image that your map is a small snow-globe world, and the area you want to see is going to be filled with water. All the entities MUST be inside the water. If it finds a hole to run into the void, everything goes to hell.
What you need to do is to load the point-file (.lin) generated when you compile. Problem, when the compiler is finished it deletes the file.
Have 3 things open:
You map (Extinction.map) in Radiant
The Map_source folder containing Extinction.map
Level Compile window
Read this section first, so you know how to do this. As soon as you click 'Compile Level', switch to the map_source folder, select the .lin file, and copy and paste it. When the compile is finished, it should of deleted the old file. Rename the copy back to Extinction.lin, then switch to Radiant.
In Radiant, with your map open, click File > Pointfile.
The redder the line, the closer to the leak. Follow the lines to the hole, if a burning red line goes through a brush into the void then delete the brush and try again.
Complicated, but a good (I think) habit to get into when leaks are not obvious and brushes appear to be flush.