Dependencies to Meshes and Textures that are NOT used

I am having a weird problem, for a very long time now in Unity, maybe as far back at 4, but I'm not sure;
When I create a scene not from scratch, or even sometimes bring in objects and then delete some pieces but keep others (a prefab or fbx) I see dependencies in my asset bundles that are for Meshes and Textures that are NOT in the scene anymore, pieces that were deleted. This happens even if it's a seemingly totally empty object that's left over.
Detailed Example; I bring in a prefab that has boxes A, B, and C in it. I delete A and B and arrange C in various ways. If I then look at the dependencies in the scene it will show textures for all of them even if only C is present and has its own texture separate from A and B.
This happens to me all the time and is a huge pain, especially as I have to make scenes that then get turned to Asset Bundles (and those bundles are often bloated, making me dissect every Object in the scene to figure out what has these weird ghost dependencies).
Anyone run into something like this and have a way to fix it permanently? or a better way of figuring out whats got ghost dependencies?? (selecting dependencies and then clicking the texture/mesh and trying to 'Find Reference in Scene' doesn't work sometimes [shows blank as if nothing references it even though it shows up in dependencies...])
VERY frustrating!!

 

check the asset store. There has been a couple tools released recently to help with cleaning up this modular workflow.

 

Which tools on the Asset Store are you referring to? I did a search and found Resource Checker and Dependency Checker...are there any others? Thanks.