I am wake scanning right now as well and have the same situation as the OP, that being Atypical Disrupted Wake Echos limit full.
I have been keeping an eye on things and just noticed one scan that came back with the "Full" message had a hint of blue underneath of it. When the "Full" cleared there was a blue tag line reading Anomalous FSD Telemetry, as in it was a double data scan.
The FSD Telemetry was collected. The ADWE's were not (obviously).
So it would appear, in my experience, that the OP's fears on this particular matter are unfounded.