I remember that when this happened to me when I was starting out mapping I didn't clip my stairs, and the nav_generate command didn't automatically realize that stairs were stairs all the time.
Try using player clips or block bullets on your stairs to make them ramps that look like stairs. This will also make sure that the view of the player doesn't vibrate as they walk up the stairs, and when people jump while going up the stairs they don't hit the vertical part of a stair and get stopped from going forward.
That being said, don't use bots to test the gameplay of your map, as bots play a lot differently to people. If you want to test the gameplay of your map, release it to the site and have it played in either an impromptu test or a gameday.