RCMP stumbled on the operation by accident. On Sept. 14, police in Repentigny, a city northeast of Montreal, accompanied Revenue Quebec officials to a metal token manufacturing factory in an industrial park to carry out a search warrant for GST evasion. When officials entered the factory, located at 119 l'Écuyer, Suite 400, they discovered coin-making equipment, buckets of coins almost ready for circulation, and raw materials.
Toonies exist since the withdrawal of $2 bills in 1996. You need to realize the fact that it has been over 10 years, someone already knew how to make a fake toonies. Normally, people don't check for fake coins because their value is so small. You can check the sound of fake and original coins by dropping them one at a time on a hard surface like wood but it will be time consuming. Especially if you have hundreds of them. Other way is by looking at the centre piece, the metal is not well bonded to the coin. You might pop up the centre with a little bit force using your thumb. I wish that can be any help. Will try to update if I found any story relating to this.
Source: CBC News, Coin Community.com, Wikipedia.