I tried doing the waypoint before, and when I touched the key it spammed the noise and the key stayed there.
You probably were unwillingly adding more keys. Waypoint mode is very buggy for the time being and occasionally will refuse to work correctly.
To ensure your waypoint is put correctly, put it away from your key to see if you're placing a waypoint and not a key (It'll have a red rectangle around it and there'll be a yellow line linking to it). Once you got it to work, move your waypoint over your key and you should be set.
Just to make sure, set up a time value for the waypoint you set up, too.