This is (probably) not a bug, but a minor feature/UI request.
A couple of times now I've had a red multiplicity systray icon on the primary machine, and the mouse not moving over to the secondary machine. The secondary machine is connected in the "Seamless" configuration, and validating the passcode succeeds with a message saying that the primary was able to connect to the secondary.
I'm guessing it's either: some sort of option that' I've turned on accidentally that locks the mouse on the primary machine (my scroll lock is not on however), or the red systray icon is an indication of some error other than not being able to connect (which shows a light grey systray icon with a tooltop that says "Multiplicity (Disconnected)") ...
... however ...
There is not a hint of a clue anywhere (and I tried the user manual) as to what the red systray icon means. There's nothing in any of the tabs of the multiplicity config dialog to say "XXX option turned on, seamless disabled" (if it's something I've enabled by accident), or - if it's an error that has occurred somewhere after/above connection, there's nothing anywhere to say what the error is: the red systray icon's tooltip is simply "Multiplicity".
FYI for anyone faced with this same situation, rebooting the primary machine fixed it both times.
Please can there be more information about the status of things in either/both of, the systray icon tooltip, and (preferably) the config UI.
If adding to the config UI, I would think that some sort of status panel with each secondary machine and it's connection state/error on connect might be nice. And, if there are "gotcha options" that can be accidentally turned on, which stop mouse and keyboard transferring between machines, then some highly visible alerts in that panel (e.g. "Scroll Lock on: Mouse/Keyboard restricted to XXX machine). I've tripped myself up once or twice with the scroll lock key years in the past.
I know the seamless config tab provides a visible indication of whether the primary is connected to each secondary, but when there is a problem, there's no information about the error there - you're left to poke at the "configure computer" dialog and figure out if it's a firewall rule blocking things, or an encryption key that doesn't match, or a passcode problem. Putting that error information somewhere relatively clear/prominent in the config dialog would be nice 
Cheers!
Daniel