I play in two different MD casinos and one lets you run it multiple times using the last card in the deck and the other disallows using the last card, meaning you can run only one turn and two rivers. Why?
It's a pretty basic rule in poker that you never use the bottom card. It's more likely to have been exposed at some point during the hand and it might be easier for the dealer to put a specific card there. A player might choose to run it twice or not if they know what the second river card will be.
Some casinos choose to go against this tradition in special cases like that or in stud/draw where it can be used to complete a round to avoid re-shuffling.
If the dealer is following proper procedure with a cut card and keeping the deck level it shouldn't be a problem but some casinos opt to be strict with the rule to be safe. Other casinos solve the problem by not burning card(s) which is probably better but might not be allowed by gaming rules.