There have been several instances during both main and side quests in which male Eivor is referred to with female pronouns.
I have compiled a list of all the times that I have encountered this bug so far:
During the quest “a little problem” in ravensthorpe, the children say “shh she’s coming” as Eivor approaches the house
When returning to Ravensthorpe for “reporting on Ledecestrescire” ceobert and randvi are speaking in the longhouse. Ceobert says “she was on her way” after randvi asks about Eivor’s whereabouts
During “kingmaker” in East Anglia, when the brawl begins the brothers yell “she called us flaccid”
Alfida says “aye, she has” at the end of “childhood sweetheart” in Essexe in reference to Eivor
I will update this list with any further encounters.