If you are recording a larger swing signal with a non-ideal voltage threshold, then small noise on the input, which would normally be ignored by a receiver at that IO voltage, could be picked up by Logic. For instance, when recording, 12-volt TTL with Logic 8 would detect any spike above 1.2 volts as a logic high, whereas a 12V part would ignore everything up to a much higher voltage. The same can happen when recording 5 volt CMOS.