Have there ever been cases where, through some sort of miscommunication or other "clerical error", a cogniscent race (either collectively or...

Do humans count?

Heheh. Um. There are times when the species are very vastly different that understanding and communication are virtually impossible.

The jury is very much out on the Hyperspace-native species known through onomatopoeic nomenclature as the Xyrak’l. Nobody knows if they’re cogniscent, cusp-cogniscent, or non-cogniscent.

But they are big enough to crush a standard passenger liner, so the general consensus is to leave them to their own business.

And then there’s the vary rare cases where a colony is encountered where the tech and society level has backslid to the level of gatherer-hunter or worse.