I don't see any easy way out of this problem (=having two substitutions for same dates. The table key effectively prevents every attempt.
I would probably just add an error message instructing that "You cannot set the same user as substitute for several profiles starting at the same date" (and some kind of hint, that they could actually change the begin date (one day earlier or whatever). Better than nothing and should be easy to implement.
EDIT: Well, of course the above will not work if the user cannot set the begin date of the substitution (which is the case with the standard UWL substitution management application). I would be interested to hear what SAP support has to say about this. (If it is possible to add a new substitution rule for same user and it replaces the old rule without any error message, this is a bug from my point of view.)
Regards,
Karri