I've been using the shapebuilder tool to clean up my artwork and suddenly it can't pick the color from the artwork correctly anymore. I had been using it with objects that have a gradient but until now it had no problem with that. When I combine shapes with it it simply turns the shapes black, though the fill color has a "?" in the properties panel.
If I choose "pick color from color swatches" then that works just fine.
I tried resetting the options for the shapebuilder tool and restarting Illustrator but the problem persists.
Which version of Illustrator are you using and on which OS? I just tried combining shapes with different gradient fills with "Pick color from artwork" selected, and it worked for me. I'm using Illustrator 24.3 on Windows 10.