We don't know the waypoint code you use for your bots, so nobody but you can tell... unless you describe your problem with more accuracy
And for the weapons, I suppose they either don't recognize the weapon they've got in hand, or they don't know which ammo is associated to it (sounds most plausible to me). Assuming you use botman's code, have you added the right lines in the weapons and weapon delay arrays at the top of bot_combat.cpp ?