Sorry, I could be wrong (maybe its not a bug):
With current settings 'save' doesn't take any resources





But from the other side - resource gathering works well:

You can always select the REMAINING resources, those which should stay on the planet or moon.
And it's intentional that the Routine Fleetsave is NOT capable to take all resources automatic. I won't change this behavior, and for sure i am not allowed to do so.