In addition to damaged journals, the library has also discovered that many texts have gone missing during the move.
Students' Union vice-president academic Alyssa Stacy said the school blames the unnoticed theft on an inferior tracking system in the MacKimmie, a problem that will be fixed in the Taylor Family Digital Library.
"Because they have a more sophisticated system, they feel that once they record everything properly in the TFDL that theft won't be that big of an issue," Stacy said. "They also have a better security system in the TFDL."
The school will also be shutting down the TFDL in the summer for three months to make repairs.
Design problems in the building had necessitated repairs over the spring and summer but up until now the school had maintained they would keep the new building at least partially open.
The university said because of the building's piping structure, it is more efficient to shut the whole TFDL down for a September opening.
The SU proposed to the Library and Cultural Resources Committee that the U of C barricade the area to the elevators and allow students access to other floors.
"We stressed the importance of accommodating the students who are doing summer classes," said Stacy. "Only the students were in favour of that."
Stacy said the nearly empty MacKimmie isn't a sufficient substitute for the TFDL after all the materials were moved out.