I think this has something to do with the reflection off of "back-facing" polygons that were created by the Boolean process. Somehow the smaller cylinder is catching the reflection of the backside polygons in the Boolean. If you create a semi-transparent material with NO reflections, you shouldn't have this problem. (Both glass and water have reflection built into them that can't be turned off) SMT

I'd rather stay in my lane than lay in my stain!