Yes, the toilet water is separate from the potable water. It's designed that way to prevent cross-contamination, also because the toilet water has an added disinfectant solution that is not intended for contact with skin.

Also, as channa said the coffee makers are fed from the potable water system, there's no reservoir like a Mr Coffee at home.

Normally, the FAs or the flight crew would notice the tank running low as part of their preflight checks and request the water to be topped up, but it seems they didn't notice it on this occasion.