SW 2015 SP4.0 but I've seen these issues on previous SW versions.
Lofting... I'm using 2 3D composite curves (created from scribed wrap edges) with 6 segments each. Loft always creates successfully 1st try. The problem is when switching to different configurations (100's defined by a design table) the start point on either or both of the composite curves will move to a different endpoint causing the loft to fail. When I switch back to the original configuration, sometimes it will loft successfully and sometimes it won't.
Surface trim... Using 3 surfaces and a mutual surface trim. When I select the portions I want to remove it always trims correctly 1st try. When switching to different configurations the portions to be removed flip flop on some configuration and not on others.
Fillets on surfaces... I select the 2 surfaces, flip the direction arrows if needed, and fillet surfaces creates correctly 1st try. When switching to different configurations the fillet direction arrows flip flip causing all subsequent features to fail.
Fillets on surface edge(s)... same as above when switching to different configurations.
The product is proprietary so I can not post the file.