In 1993, Legends of the Hidden Temple hit Nickelodeon airwaves, and has since been widely considered to be one of their best game shows. While no aired episodes are missing, there was a Temple Run (or possibly an entire episode) that never aired at all.
According to host Kirk Fogg on the web series The Garage Show with Jeff Sutphen, there was a female contestant in the temple; the episode, season and team weren't specified. She had been having a meltdown in [aptly] the Pit of Despair. The cameras were still rolling, however, she eventually vomited everywhere and they had to stop to re-record after everything was cleaned up. 
According to Kirk Fogg on E! News' Celebrity Sit Down, she was crying and she was upset after that and they had to fix her and get her happy again.
No one knows why it happened, however it is possible she was overly tired as Temple Runs would be recorded during the night time hours.
There isn't much more information on this than what's already been stated, but despite the [slim] chance of it still existing, it can be easily assumed that this was confiscated due to the fact the take couldn't be used.