I'm running the Male route, and gave Jayne muscle and not a penis. I don't even think giving her a penis was even an option in that route.
MaleMain.rpy Line 2548
scene BW8MG1
needs to be changed to
scene BW8MGF1
Otherwise, it makes Jayne show up with a penis even though she isn't supposed to have one there. I think BWMGF is supposed to be there instead, though the variables in MainImages.rpy refer to it as BWMGF1, which is wrong. I had to rename the webp in the game\images\Main\0.8\Vari\ folder to keep the game from throwing an error from my fix.
Also, at the new sandbox events at school, people kept referring to the MC as "she", even though I'm playing the Male route.