The attached save game is set up to reproduce this bug. Each of the three tanks on the left start containing 120 L of paint. When you connect the red pipe to the left-most mixer, the volume in the tank will start to drop, but the reported volume of red in the mixer (and the animation) won't start to rise until the tank is down to 60 L. Once the red tank is completely empty, 120 L has left the tank but the mixer says it contains only 60 L of red. The same happens when you connect the green tank to the mixer input.
The mixer will then start a mixing cycle and say that it's produced 120 L of yellow paint. But when you connect the output of that mixer to the adjacent storage tank, the storage tank starts to fill but the reported volume of yellow paint in the mixer doesn't decrease until the storage tank has reached 120 L. By the time the mixer output is completely empty, the storage tank will contain 240 L of yellow paint even though the mixer claimed to have mixed 60 L of red and 60 L of green to produce 120 L of yellow.
It can be seen therefore that no paint is actually going missing, because 2* 120 L went in and 240 L came out, but rather the contents reported for the input and output tanks are only half of what actually went in and out.