A necessary condition for a subset $\Sigma\subseteq S_n$ to be a transitive permutation group of order $n$, is to be... transitive. Is the best algorithm to check $\Sigma$'s transitivity faster than the best algorithm to check that $\Sigma$ is a (sub)group?
Context/motivation. If the transitivity check needs no more than $O(n^2)$ runtime, I guess that the same holds for checking the non-associativity of a Latin square of order $n$. See here for further reference.