St Mirren, the reigning holders, had a goal ruled out when the referee judged Eseosa Sule to have fouled goalkeeper Aston Oxborough before Samuel Ramos put the ball in the net.
Two minutes from the end, Dunfermline’s Chris Kane converted a penalty after Marcus Fraser was penalised for a foul on Keith Bray.
St Mirren said they will fully review the notice before deciding on their next steps and will not comment further for now.
According to the St Mirren Mercury, McLeish maintained that his on-air remark about Murdoch was intended as “tongue-in-cheek.”
Despite the defeat, St Mirren topped the group, with Dunfermline progressing as runners-up. However, the loss left St Mirren unseeded for the last 16, resulting in an away tie at Rangers.