Chances are the extra payments to the players were claimed as a deduction in the entity's making the payments tax returns thus they would have lodged something with ATO letting them know they were paying the players something.
For all we know they actually issued PAYG Payment Summary's to each of the players and lodged them with the ATO.
The ATO couldn't care less if the payments came from Brown Paper Bags Pty Limted ATF The We Didn't Know Anything Trust. As long as they declared the income it is all good.
Weren't they invoiced as consulting fee's?
If yes, then its likely the invoicing entity claimed the bogus consulting fee's as a deduction, but that doesn't mean the receiving entity has declared the income received.