- drag and rejoin one of the connectors to the correct system. The system should regenerate.
- Cut one of the problem elements, then Paste Align - Same Place. After this, you will need to use Connect Into to get the element connected with the system. You might find that doing this on one Fitting will force a regeneration on the entire system, fixing all Duct Fittings with this problem at once.
I have put together a quick screencast for each of these methods:
If you have another way of fixing these problems, feel free to comment. Thanks!