If you find that bots in your server are failing to move around your custom map it likely means you need to generate a .nav file for them. A .nav file defines the "walkable areas" and is required for AI to properly navigate the map. You can use these simple steps to generate that file.
Login to your servers RCON using the "rcon_password mypassword" command
Type "rcon sv_cheats 1"
Enter "rcon nav_generate"
This process can take a few minutes depending on the map and can cause server lag. Once this process finishes it will automatically change to the next map in rotation. Repeat this process for all of the needed maps or if you've finished disable cheats by typing "sv_cheats 0" into console.
Additional information on Navigation Meshes is provided on Valve's wiki
@Kraze^NFo> Juski has a very valid point
@Juski> Got my new signature, thanks!
@Kraze^NFo> Out of context!
@Juski> Doesn't matter!
@Juski> You said I had a valid point! You can't take it back now! It's out there!