The Wikipedia article on Cuckold indicates that the biological phenomenon of brood parasitism was known in the middle ages. (I suspect it may have been known in other cultures as well, but I can't say for sure)

Although observing such behaviour doesn't require much in the way of advanced technology (though binoculars can help), I assume observing this behaviour would take a lot of time, and the birds (both hosts and parasites) are of little economic significance.

I tried searching about how brood parasitism was discovered, but I most of the hits about discovery were about whether or not the hosts discover the parasitism occurring.

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    $\begingroup$ Most likely a simple case of people observing nature while they were out doing other things, such as raiding birds' nests for eggs and seeing a strange (cuckoo) egg in the nest. $\endgroup$ – Spencer Feb 18 '17 at 3:03

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