Two parallel motor under PWM now have slightly different speeds
You cannot expect two open-loop motors to have the same performance - even if matched initially they may age differently.  I'd especially expect that with brushed DC motors where brush wear can be a part of aging, or any system with sleeve-type bearings. 

You can used closed loop control monitoring a rotary encoder to slave both motors to a desired rotation rate, or one to the other other, or switch to stepper motors, however electronics may not be the best solution.

Instead, Lab-grade peristaltic pumps typically allow stacking multiple pump heads on a single motor, which will get you identical rotation rates and with the same size tubing fairly close flow rates.

If that is not close enough (some fluid property making pumping different?  one line pulling air?), you can either go back to closed loop and have a manual differential trim control to run one faster, or you can build a closed loop controller that watches some liquid level sensor, or perhaps a scale under the experiment.