When I try and test a 3 way junction it will eventually spawn a train heading to the output that isn't there.

Are you using the latest version? Is that on a lane not connected to the intersection?

I'm on version 1.1.0 of the mod and version 1.1.104 of Factorio, I completely deleted all the stations on the South side (I also tried with the North side removed and got the same result).

I'm on version 1.1.0 of the mod and version 1.1.104 of Factorio, I completely deleted all the stations on the South side (I also tried with the North side removed and got the same result).

Don't delete the stations, just don't connect one direction.

So I tried that overagain and the test runs fine even with deleting stations.