This is a Latin expression meaning "of uncertain position" or "of unsettled place" and refers to a taxon with contentious relationships. This is an invariable expression and does not admit singular or plural.
From classical Latin:
sēdes, sēdis (gen plur. sēdum) - Feminine Noun of the Third Declension = a seat, place, spot, base, ground, foundation, bottom
incertus, a, um - Adjective = of things, not fixed, unsettled, undetermined
Both words go in the genitive case, forming the expression
incertae sedis = of unsettled place
For better understanding, a simple analogy can be made using nouns of varied declensions:
incertae patriae = of an undetermined land (patria - 1st fem)
incertarum patriarum = of uncertain lands
incerti loci = "of an unknown location" (locus - 2nd masc)
incertorum locorum = of unknown locations
incerti nemoris = of an uncertain pasture (nemus - 3rd neut)
incertorum nemorum = of uncertain pastures
Many authors, especially those whose languages do not have declensions, make the wrong analogy:
incerta - feminine singular
incertae - feminine plural
Which is indeed, correct, but the trick here is that in Latin First Declension, the Plural Nominative is equal to the Singular Genitive.
Also common is the mistake "insertae sedis" (with S), where people mixup with the verb "to insert".