The Croatia international was taken off on a stretcher in the 117th minute of the Reds' League Cup penalty shootout victory over Carlisle at Anfield.
"He landed awkwardly but fingers crossed I don't think it's as bad as it looked," said McAllister.
Roberto Firmino also went off, but McAllister said he "seems fine".
The Brazilian forward was replaced in the 35th minute.
"Like Dejan, he landed badly," said McAllister.
"It was just a ball he went up for and he's landed on the base of his spine, just on his lower back."
Liverpool, who are 13th in the Premier League, host 17th-placed Aston Villa on Saturday (15:00 BST).
Liverpool are hopeful defender Dejan Lovren's injury is not as bad as initially feared, says assistant manager Gary McAllister.