Make sure the assembly is active and press Ctrl+F7 and you will see a diagnostics showing if something is wrong with the geometry (make sure you have a C:\Temp folder if the pop-up never comes).
Trying a Manage (tab) > Rebuild All has a slim chance of helping too, if you try again after that.
Also try to select the bodies in a different order to see if that helps.
"That can happen if you have surfaces that are nearly coincident, or where one surface intersects almost but not quite at an edge of the other surface. If you can post the part, I can have someone look at it to see if they can narrow down the problem."
https://forums.autodesk.com/t5/inventor-forum/error-while-deriving-assembly/td-p/2491383
