@ KWo: The problem is not the waypoints - it's the lift itself! It kills bots just like that door in cs_arabstreets! There's nothing you can do about it - if a bot is inside the lift, there's a 75% chance it will die, period. Even if you spawned a bot directly into the lift, it would be likely to die as soon as someone pushes the button, no matter if there are waypoints or not or how those waypoints are laid out. It's a fault in the map. Thus, it's useless to "complain" on the bug report forum.
@ MarD: Yes, as KWo said. You will find it in the waypointing menu. It will define the distance where connections between nodes are created automatically in several steps from 100 distance units up to 250 (which was the default with PB 2.5). This feature is very useful when waypointing narrow areas: You can lower apmd settings to, let's say, 120 units and place waypoints rather closely together without having overlapping connections with waypoints that are far away.
It's also great for camp waypoints: With the old WP system, you had several looong connections leading to a camp WP, and if that camp WP was a crouched WP, bots would crouch-walk an insane distance to approach it. Besides, all those connections would clutter up the connection pattern in the room. Now, you can first waypoint the room, then lower apmd settings, then add a camp WP in a corner, and only a short connection to the nearest waypoint (if it's inside the distance covered by apmd) will be drawn.
Makes everything very neat and clean, a definite must-use!
Play around with it; as soon as you get the hang of it, you'll love it! I generally use low apmd settings in narrow or tricky areas and long apmd settings in open spaces. That's partly because shorter connections allow for more precise bot movement, which is helpful in some spots.