While finishing up the last stretch of Aquila's storyline, I ran across two cosmetic bugs.
First, whenever the skeleton hopilites perform their critical hit animation (which is the standard hit animation for the more heavily armored hopilites) their shields become inverted for the rest of the fight.
Secondly, the few bits of dialogue that feature Sara Steele (rank three, mouse corsair) near the end of Aquila do not display her correctly. Instead, the name above the text box is shown as "Mouse Fencer" and the image in said text box shows the mouse fencer from Scrimshaw.
Both have happened every time the possibility for them has arisen.