Like many questions here at SBPS, this one falls under the category of "You do whatever you want."
We don't like to interfere with individual contests, especially with questions about how to pick who won prizes and what to do in case of confusion.
I would say that it typically helps to be as transparent with your players as possible. Communication is key. Letting them know ahead of time that "any prizes won by an empty box will be donated to charity" is much better than making that announcement after the fact.
Personally, I would recommend donating any prizes won by an empty square to the charity or fundraiser that the contest is aligned with.
If this is just simply a contest among friends, another popular alternative is to split the prize among the other winning squares, or to roll up any unclaimed prizes into the grand prize (typically the Final Score) -- however, be careful as the Final Score may also belong to an empty square.
Get creative - there aren't any rules that we enforce with regards to this, so if the above suggestions don't suit you, make something up yourself. I would only stress again, be transparent with your players to avoid common headaches of mistrust.