Yeah, I remember hearing about this! Wasn't there also a creepy case where an evolved circuit involved FPGA that weren't attached to anything else in the circuit, and yet were still needed for the thing to work properly? I seem to recall it similarly involved electromagnetic interference.
They drew a graph of any units on any connected path from input to output, and then ran a search to see if any others had any effects, by clamping random units' values to 0 or 1 and seeing if that degraded the result. They found that one unconnected unit in particular degraded performance significantly (the bottom/right gray-colored one in Fig. 7): it had several active connections routed through it, but its own output went nowhere. So they hypothesized that it was modulating the signal in a way not captured by the mathematical abstraction of the FPGA as a digital circuit.
