I'm a believer in having systems in place for things. Obviously you can't predict everything, but you can learn from past mistakes.
Systems should be written down, so if anyone questions your decision, you show them the written documents and everything is above board.
I think a few things could be made into a system with documentation that would be part of the rules set of xzy tournament, that if a player or fan wanted to, they would have access to it on the rules site of the tournament.
These are my ideas, but they could easily be changed. The main point is to have them written down in place.
1. Decide if a paid player is a no-show come draw time, whether to replace him.
2. Decide if a paid player is a no-show, come match time whether to replace him.
3. If you decide yes for #1 or #2, then go down the list of alternates that are at the venue. First come first serve. Must have cash money in hand. After alternate is in and paid, refund the original entrant his money at the end of the tournament. (Or, make it policy not to refund him if he did not give prior notice, and use the extra funds in the pot).
4. Sometimes administrative mistakes are made, and too many players are signed up. Make a procedure on how to handle that. Cut them out and refund them, or expand the bracket to 256 to accommodate those extra few players. (or insert another idea).
Again, the main thing here is not which rule to put in place, but to have it written down where anyone can access it if they chose to. Then, there can be no accusations of favoritism, or underhandedness, etc.