Mark Salzmann, chairman of Red Docs Munich, a Bayern Munich supporters’ group which helps care for the memorial, said his mother discovered the damage while driving past.
Salzmann said a glass sculpture originally presented to Munich’s former mayor, Dieter Reiter, was among the stolen items.
His group collects tributes left by visitors from around the world and places some of them in the display case.
He said the objects were unique and could not easily be replaced, but the group was discussing possible replacements with the foundation.
Ahmed said it was still unclear exactly how many medals were missing.
He said Manchester United had offered to pay for repairs, but the foundation had already agreed to cover the costs itself.
The broken glass was replaced on the same day, according to the foundation.
Ahmed said supporters of Liverpool, Manchester City and Leeds had also sent messages of support.