Try adding the fact (and the supporting documentation) to the wife instead of the husband. The system always tries to attach documentation to the earliest marriage date, regardless of the spouse name.
So, if the ancestor is John Jones and he first married Susan Smith and then Elizabeth Black, create a "marriage fact" for each marriage. Then, when attaching documentation for each marriage, attach to Susan rather than John, and to Elizabeth rather than John. Unless each of the wives also had multiple marriages, that should take care of the problem. If the documentation is under John's name, just click the "attach to someone else" link, and search for Susan or Elizabeth, which will attach it to her and also to John as her spouse.
Good luck with this - it's just an annoying quirk of the system.