I noticed this problem the most while playing on arena, with Han/Yagura/Mei/Fire Main team (which I do a lot and notice this issue often):

- for second round, to cast Mei's mystery I get 40 chakra points together from both main's and Yagura passives: after Yagura add chakra I immediately click on Mei mystery, before she does her standard and many times there's no reaction at first but then her mystery goes off in next round, which make it easy to block as she's on last position;

- also noticed problem with mystery delay on other ninjas, mostly on last position in lineup- even if skill is choosen before they do their standard attack, sometimes it doesn't go off untill the next round;

Noticed this issue on arena, matsuri and sage battlefield.