I am fairly inexperienced with elliptic curves so there might be aspects of my question that may need better wording but let me know if there are any issues:
Question: Say I have an elliptic curve over $\mathbb{F}_7$ and this curve has 12 points. I take a subgroup of size 3 and I quotient the curve by that subgroup. Magma and Sage can easily tell me the equation of the curve where the quotient lives. Not surprisingly, extra points pop up when taking a quotient that where not defined over $\mathbb{F}_7$ but become defined over $\mathbb{F}_7$ when you take the quotient. So the curve they spit out may (and usually does according to my random sample) still have 12 points.
What is happening on the function field side? Is the function field of the original curve an extension of the function field of the other curve? If not what is going on?