Neither Leverkusen nor the referee appeared to notice that Schalke defender Ciprian Marica was stricken in his penalty area when the visitors scored their opening goal.
The Romanian was hurt in a clash with Stefan Kiessling as the Schalke defence cleared away a corner. Leverkusen won back possession, the ball was fed to Lars Bender on the right and his cross was headed in by Simon Rolfes at the far post.
Schalke's players surrounded the referees and jeers rang round the stadium.
"I think it was a foul on Marica but I don't want to comment on whether they should have kicked the ball out of play," said Schalke coach Jens Keller.
Football has long struggled with the issue of when to stop matches to treat injured players.
The problem started when teams began to voluntarily kick the ball out of play to allow injured players to be treated.
Initially seen as a sporting gesture which prompted applause from fans, it soon became an unwritten rule that play should stop when a player went down injured, even if it meant breaking up a promising counter-attack.
This in turn became abused as players feigned injury while still expecting their opponents to kick the ball out.
UEFA has issued guidelines that only the referee can stop play but there were still instances at Euro 2012 of players looking to the referee to stop the game when an opponent went down injured, sometimes kicking it out themselves.
In Italy and Spain, players are still expected to stop play if a someone goes down.
Arsenal manager Arsene Wenger said last year that his players sometimes ignored instructions to keep playing as they were afraid that playing on might make them unpopular.