"This one character is specifically referring to this other character not by their name, but the title of their role. I'm going to change the dialogue so that this is no longer the case." Of course, this would be based less on pre-established character and more on the content of the line at hand.
"We're starting in the middle of the story with this character already here."
"She seems to be calling the characters by their jobs sometimes"
"Sometimes? You've seen her call them by their names?"
"Yeah, she does it all the time in this video game we're doing."
"Oh, then it must not be too important."
So lets end this round of "Chastise FUNimation for mistakes they admitted to and went out of their way to fix."