By default, if you select all connected geometry and create a component, the component will automatically replace the loose geometry. If you select only some of the connected geometry to make the component, the default behavior is to create the component but leave the loose geometry. If you tick the box for Replace… the loose geometry gets replaced with the component. And this preference is remembered for future components.
It’s probably best to get in the habit of modeling the geometry for one part and make that a component before you move on to modeling the next part. This eliminates altogether the issue you were having and prevents potential problems. For example, here I’ve drawn to boxes side by side but all is loose geometry.
I select the geometry for the left hand one and make a component making sure I replace the selection with the component.
Then I repeat that for the right hand box.
When I move the left hand one away and rotate it, you can see that it has captured the face where the two boxes met. Since that face was added to the first component, it isn’t available for the second.
If the left hand box had been component-ized before even beginning to draw the right hand box, this wouldn’t have happened. The right hand box would be complete.