Cilic broke down in tears at 6-4 3-0 down and was spoken to on court by a doctor.
It was unclear what exactly had gone wrong with the doctor returning again at the end of the set, which he lost 6-1.
Becker, working for the BBC, said: "We've got an explanation of what went wrong.
"He had a huge blister on his foot and couldn't walk anymore.
Marin Cilic broke down in tears during the final against Roger Federer
Marin Cilic took a medical time out to get some treatment
"I hope they've fixed it.
"I just hope for the sake of the spectators the final will be more of a match now."
A medical timeout was called at the end of the set, during which Cilic had strapping removed and reapplied on his foot.
Marin Cilic breaks down in TEARS during Wimbledon 2017 final Sun, July 16, 2017
Marin Cilic broke down in tears during the Wimbledon final against Roger Federer.
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Appearing alongside Becker in the commentary box, Andrew Castle said: "There's a certain amount of turmoil in his head now.
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"He's a little embarrassed. It's only been going on an hour and 18 minutes.
"He's a little disappointed with how hes playing so far."