Assumed Pensionable Pay when additional run results exist

We recently encountered an issue where assumed pensionable pay was being calculated as lower than expected, this was caused by an employee having two runs for one period within the APP reference period and APP logic looking for a number of runs as the value to divide total pay by, rather than number of periods, the client does not use supplementary runs or any elements which are processed separately from the main run, but it raises the question of if a business does process multiple runs for an employee for any reason and this falls within a reference period for