If the school has requested or recommended that the letter come from a teacher in a stem subject, then I would see if it can be changed. Our school uses Naviance and the GC definitely gets to choose. Thankfully, they explain the year before apps that they will pick the one(s) that are the most detailed, most personal, etc, in situations where they cannot send all. Unfortunately parents still sometimes don’t trust the process and demand certain ones are sent—school usually just moves on and sends the requested one. We never did that—but we had gotten the clear info that they pick based on specific details. D21 is a history/humanities kid. She had an English, History and science rec. The science one went everywhere and the history only to places that allowed 3. She did very very well in admissions and I suspect her struggles then rising to the challenge of the very difficult physics class led to a much more detailed helpful rec than the history one where she cruised through the class and was always at the top. Or the physics teacher just writes them better/more detailed.
D23 needed to send just one of her 3 to a merit scholarship program at a school: the counselor told her that they’d pick the most in depth personal one with specific details that would match to what this leadership-type merit scholarship wants, and again we were mildly surprised which one it was. I am sure there are many other reasons one rec is “better” than another—sorry the GC wasn’t honest with you and said it was random. You could see if some gentle prodding will help answer why they sent that one.