The aim of this paper is two-fold. We first prove several new interpretations of a kind of $(q,t)$-Catalan numbers along with their corresponding $gamma$-expansions using pattern avoiding permutations. Secondly, we give a complete characterization of certain $(-1)$-phenomenon for each subset of permutations avoiding a single pattern of length three, and discuss their $q$-analogues utilizing the newly obtained $q$-$gamma$-expansions, as well as the continued fraction of a quint-variate generating function due to Shin and the fourth author. Moreover, we enumerate the alternating permutations avoiding simultaneously two patterns, namely $(2413,3142)$ and $(1342,2431)$, of length four, and consider such $(-1)$-phenomenon for these two subsets as well.