In my assemblies I use custom made security screws for our products, and there's this one screw that most every time I use it, and then revert back to the model, it is replaced with similar screw from the toolbox. I don't think there's any connection between the two.
Was the problem screw created by taking a toolbox part and modifying it? That can create problems such as you're experiencing.
So I think I figured it out Go to -configurations manager -right click on the configurations, and click properties -Go down to Bill of Materials options click on the down arrow and click on Document Name