"One time Chuck [Lorre] busted us hiding behind a car in the parking lot. It was after a show ... and we ducked down, like kids hiding from their parents!"
While Kaley Cuoco very vividly remembers being busted by her showrunner boss, he seemed to be very preoccupied with whatever was going on with the show, and joked he didn't have the "emotional bandwidth" to deal with seeing his actors hook up.
He also said in the book:
"I can't remember that. That might be one of those things I compartmentalized like, 'I can't deal with this, I don't have the mental, emotional bandwidth to deal with an on set romance."
Cuoco seemed amused by the story and called it "such a Chuck answer," which makes me think there are probably other incidents in the history of The Big Bang Theory in which the showrunner simply buried his head in the sand.
Meanwhile, while the two were seen making out on set, the actress would like everyone to know the PDA stopped there. As she bluntly put it, "[we] never even had [sex] in our dressing rooms."