In Ninja Turtles 2 (1991), we see the foot capture the TGRI professor as he is processing the last canister of Ooze. Shredder forces the professor to use the Ooze to create Tokka and Rahzar, but during the construction site fight scene (before eating the donuts), Shredder holds up a full canister of Ooze. Where did that come from? It was made clear that there was only one left and the amount of Ooze we saw the professor use to create Tokka and Rahzar was significant.
As far as I can tell, it's not a different canister, it's the same canister as earlier in the film. Note that we never actually see it being emptied, only what appears to be 'ooze' traveling down the pipe into the animal enclosures.
Also, there's some bubbling chemicals that the Doc obvious thought were important to the process and some sort of distilling chamber. It's reasonable to assume that he only used a very small amount of the ooze to prime a solution that's less poisonous than simply feeding the animals the raw product, leaving the majority of the original ooze in the canister for later use.