The Warriors were dealing with a host of issues that materialised throughout Game 2.
Kevon Looney went down with a chest injury while Andre Iguodala and Steph Curry were also coping with problems.
But then Thompson went down midway through the fourth quarter, clutching his hamstring as he walked off the court.
It appeared as though the 29-year-old suffered the injury after attempting to draw a foul on a three-pointer.
He fell down awkwardly on the play and while he continued to play, the hamstring eventually hurt too much for him to continue.
However, despite all the injury issues, the Warriors kept the Raptors at bay to pull off the win and tie the series.
Attention now turns to Game 3 with the NBA Finals heading to Oakland.
There will be a few days for players to recover and Kerr insists Thompson’s spirits are up about being able to return despite his hamstring issue.
“Klay said he’ll be fine, but Klay could be half dead and he’d say be fine,” he said.
“He pulled his hamstring.
“He thinks it’s minor, so I don’t know what that means going forward.”