Eisa made way for Theo Robinson shortly before half time as he was unable to continue after pulling up with a hamstring problem.
The extent of the injury is not yet know but Adams admits it is the same hamstring that has kept Eisa out for the majority of the season.
Adams also confirmed that Charles Vernam suffered a hamstring problem in the midweek defeat at Tranmere Rovers.
"I don't know the full extent yet but he said that he felt the same hamstring," said Adams of Eisa's injury.
"That is something that is obviously concerning. For him to come off and for him to feel it, it can't be good. We lost [Charles] Vernam in the week to a hamstring injury.
"We have had a lot of hamstring injuries this season."
Adams admits it is the worst injury crisis he has faced in his managerial career and that he has explored the reasons behind the Bantams' injury problems.
He added: "I have never had it in my managerial career. There has to be an issue as to why we are having this reoccurrence of hamstring injuries.
"We have looked into it but we haven't come to any conclusion on it."
Bottom-of-the-table Scunthorpe took the lead against City on Saturday before Yann Songo'o rescued a point with a second-half equaliser.