Connecting USB-powered Beaglebone to car's CAN bus through OBD connector using common signal ground
You would think because of the differential nature of CAN and the fact that you are not drawing power from the OBD port, it would all work fine without the common ground reference.

But, you are then at the mercy of your 2 floating grounds. The CAN transcivier will have an upper limit of the common mode voltage it can tolerate. If at some point the disparity between your floating grounds is large enough to exceed that, you can damage your transcievers. This is not something you can control: so yes use a common ground.

Edit 1:

If however you MUST use floating grounds then consider other (more expensive) transeviers with isolated inputs.