Summer signing Curtis Main was left out of the squad for the 5-0 thrashing of Chikhura Sachkhere as a precaution having suffered tightness in his thigh on the eve of the tie.
Main is set to be given the go-ahead for Sunday’s Premiership opener against Hearts at Pittodrie on Sunday.
McInnes said: “Curtis reported with a little tightness in his thigh and we resisted the temptation to put him on the bench because we have another game on Sunday.
“It is unfortunate as he felt a little twinge in training.”
Striker Stevie May was named on the bench against Chikhura Sachkhere after his move to St Johnstone collapsed last week.
Dundee, St Mirren and Kilmarnock are still tracking the 26-year-old who still has two years left on his Dons deal.
McInnes said: “Stevie is still with us for now.
“That may well change but while he is still in the building Stevie will still be part of the squad.”