At work we keep our instrumentation circuits separated from power circuits which at work are 600 volt AC. Do we need to keep for example the PWM wiring separated as best we can from motor power wires since the motor power wires will see increases and decreases in DC current ?
I’ve never seen an issue on a robot due to interference from an adjacent power wiring, so I don’t think it’s critical. However, it never hurts to explain the theory behind it to your students, and start them off doing it as a best practice!
We have seen a few instances of interference between power lines to powerful motors and smaller, more sensitive lines (most often sensors). It is not required by the manual to separate your wires in this way, but if you have the time, the capability, and the know-how, I do not see how it could possibly be a bad thing.
There are plenty of teams who will have a wire nest and a fully functioning robot, but organizing and separating wires will not only help you troubleshoot and fix things, but it makes it significantly easier on the inspectors to check all of the electrical connections are in their correct place.
At work, you are separating the low voltage instrumentation circuits from the 600 V power circuits to prevent noise being coupled from the power circuits into the instrumentation circuits. They are also separated for safety reasons, to prevent someone touching the low voltage circuits from getting electrocuted by the high voltages.
In your robot, all the circuits are low voltage so there is generally not the risk of electrocution. There is still the risk of noise coupling from the power circuits into the control and sensor circuits. If the power wiring needs to run parallel to some of the control/sensor wires, providing about an inch of separation should be sufficient to keep the noise out. It is okay if the power and control/sensor wires cross at right angles because the noise coupling in that configuration is inherently not very strong.
In your robot, the precautions for the power wiring should be applied to ALL of the power wiring, not just the wires on the outputs of the motor controllers. The output of the motor controllers has PWM voltages and (large) PWM currents that can couple to your control/sensor wires. The input of the motor controllers also have large PWM currents that can couple to your control/sensor wires.
While it is a good idea, don’t go overboard. Prioritize which power paths to keep away from signal wires, such as the high-current connection between the battery and the PDP and the wires carrying power to a few high-load motors (the drive motors, for example). These paths are best kept as short as practical to begin with, so (ideally) it shouldn’t be too hard to avoid them. If you need signal wires to cross over these power wires, do so at 90 degree angles to minimize interference. That should be sufficient to substantially reduce the chances of any issues.
It is ironic that the “birds nest” wiring inherently is less likely to experience noise coupling than the neater wiring schemes. due to how the physics of it all works.
Best practice is to keep them separate. Motor wiring has considerable brush noise that will exceed PWM signals by several volts and runs ‘DC to green light’ in frequency. If you need to run PWM cables across motor wiring, it is best done at right angles to minimize the crosstalk.
Unless your wiring has something like this going on you should be fine 
https://i.imgur.com/EdOP0jE.png
