I should have clarified in my original post. I already had a Marriage Fact for both marriages, both with the correct spouses and correct dates. The second marriage already had a source linked to it.
The new marriage source was for the first marriage, but the hint compared that date to the second marriage date.
I have tried to add it to the spouse in other cases, but noticed the same thing as you mention. It does not always add the source to both people.
Thats why I think having the ability to select which fact to update and/or add the source to would be very helpful. Also for the reasons of occupation or other bits of information from Census or Draft or other records that don't apply to the Name, Birth, Death, Marriage or Residence facts that are given.
I never could figure out how to link a Census source to different facts, other than what it linked to based on the review screen. Because clicking that source never took me to a detail page, just to the Census record itself. Sources I created manually do take me to a detail page, where I could edit and link it to other facts.
But I did as you suggested, going into the detail from the Source Citations page, and that worked great. So I think that will be a workaround for most of the issues I listed.
Still, it would be nice to be able to do that at the time the record is linked.