"Very disappointing," Khune said on SABC Sport.
"Because that could have been communicated before the game started [that Kaizer Chiefs needed a two-goal margin to seal qualification].
"The players should have been told that ‘guys, if we were to compare apples with apples, this is the juice you might get," he added.
"They focused on themselves, yes, it’s very important to look at your own results and performance but again, this table is too tight.
"They should have known better to say guys, let’s look at the comparisons in terms of goal difference.
"It is very disappointing that this was not communicated to the coach, the players should have been told they needed that extra goal," he said.