Covers have been erected over alcohol, PayPoints and lotto tickets due to licensing issues ahead of the rescue deal.
Morrisons did not say when the issue will be resolved.
A spokesperson said: “It is something impacting all stores and we are working at pace to apply for all the correct licenses”.
Morrisons will pay off McColl's £170m debts and take on all 1,160 shops, including 17 in South Yorkshire.
In Sheffield they are at: Rural Lane, Wisewood; Ecclesall Road South, Hutcliffe Wood Road, Margetson Crescent, Low Edges Road and Green Lane, Dronfield.
It has stores in Rotherham at Whitehill Lane; St John’s Green and Oaks Lane, Kimberworth Park; Broom Valley Road, Kilnhurst Road, Fleming Way and Wales Road.
It also has Green Spring Avenue, Barnsley; Cuttholme Way, Loundsley Green, Chesterfield; Union Street, Harthill and Thomas Street, Swinton, Mexborough.