Central defender Cresswell left the field with a shoulder problem while Hurst suffered a recurrence of a back injury as Paul Sturrock's side missed the opportunity to host Chelsea in the fourth round.
Sturrock is unsure as to how long the pair will be out of action but admits he is concerned.
He told Echo News: "Until they have the scans we won't know how serious the injuries are.
"It doesn't look good at the moment but we're obviously hoping they won't be too bad."
The Shrimpers boss has confirmed that midfielder Marc Laird will be out for two to three weeks with a pulled hamstring.