I've run into it...or something similar. Reported during beta 8.1 and beta 9.0, but still not fixed.
😞
I specifically ran into it subtracting a profile object (created by Profile) from a beam to give a carved beam end.
The workaround I've had when I encounter this is to change from "Use Their Own Attributes" (my usual setting) to "Inherit Attributes of Operator", and to change the operator material to be the material of the target.
Karl