Partially Hollow Stud?

As the GIF shows, at some point I created a stud which joined onto another. Looking back at my design, I noticed that it was overlapping but with the overlapping portion being transparent. How do I make the whole shape solid again?
This problem has been duplicated with all other similar groups of studs, I assume where I have re-sized at some point.
When I stretch the stud to extend or contract, the void tends to expand or contract in proportion to the movement.
How can I correct this?

you must have left some geometry inside your component. It can be a face, a line or even a point that expands your component bounding box, making you feel it has a transparent area. Simply edit your component and erase everything which is above the end of the solid part

Edit : looking closer to your gif, it seems it is indeed a point (C-point) that lies a the end of a guideline. Remove them

Bingo! That solved every problem in two clicks, thank you.

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