By a general theory $X_1(13)$ is smooth over $\mathbb{Z}[1/13]$, and so is its Jacobian $J$.
And the hyperelliptic curve given by an affine model $y^2 = x^6 - 2x^5 + x^4 -2x^3 + 6x^2 -4x + 1$ is $X_1(13)$.
However, according to MAGMA, $J$ is bad at $2$.
What is wrong with my argument?
Here is my code:
P<x> := PolynomialRing(RationalField());
C := HyperellipticCurve(x^6 - 2 * x^5 + x^4 - 2 * x^3 + 6 * x^2 - 4 * x +1);
J := Jacobian(C);
BadPrimes(J);