To reproduce:
1. Open attached project
2. Open test scene
3. Press play
4. Select Debug Wire object

In this test scene you can toggle the "Use Sphere Cast" bool to run the CheckConnection() method in DebugWire (using either a sphere cast or ray cast depending on whether or not the bool is true).

5. Notice that when "Use Sphere Cast" is toggled off (ray cast is used) two element is detected.
6. Toggle on "Use Sphere Cast"
7. Notice that when sphere cast is used only one element is detected
8. In scene view move away DebugWire game object from Cubes
9. Create two duplicates of one of the cubes and place them next to each other
10. Select DebugWire and toggle "Use Sphere Cast"
11. Move DebugWire on cubes so that all 4 cubes would be in contact with DebugWire (before moving make sure that "Use Sphere Cast" is toggled off)
12. Toggle on "Use Sphere Cast"
13. Now all elements on DebugWire are detected by ray cast and sphere cast