Make sure when you select what you want to weld, it's only that part. It sounds like maybe everything within the shape was selected to. You can select one at a time by holding the Ctrl key and select each part one at a time.
If you are using Silhouette Studio, what you see is what you get meaning whatever you see on the screen is what will print.
Under A Cherry Tree
has great tuts on welding!
Hope this helps. Any more questions, please ask!