1. are you sure you want to cut at assembly level (in most cases posted here the answer to that question is - No)
2. are you referring to the preview highlight (preview convention is green - add, red - subtract, blue - intersection, subtract only option available at assembly level)
3. is your part actually red when operation complete (as indicate - at least post screen shot if not actual assembly)
4. can you reproduce this behavior in a simple example assembly?
-----------------------------------------------------------------------------------------
Autodesk Inventor 2019 Certified Professional
Autodesk AutoCAD 2013 Certified Professional
Certified SolidWorks Professional