When you paint a certain cosmetic and are unable to select it with your Bone Merger afterwards, first, flail your Physics Gun all around the cosmetic until you find where it can be grabbed, (usually somewhere around where the green circle used to be). Then while looking straight through the cosmetic at where it can be grabbed, you can select it there with your Bone Merge tool.

Note that its gabbing point may change if you move it around too much and letting go afterwards.

Let me know if this helps!