Some time ago Jasonking posted on our forums an NXT-G addon that cleans bad wires from your diagram (these are the ugly black dotted lines you need to hunt sometimes in your program for it to compile).

Setup Instructions:
Copy the file RemoveBadWires.llb to a directory engine/project under your NXT program directory. If this directory does not exist, create it first. Restart NXT-G software. If you followed this correctly, you should have under Tools menu an option “Remove Bad Wires…”.