Let $X$ be the blowing-up of $\mathbb{P}^2_{\mathbb{Q}}$ at four rational points on a line. Can one show that $X$ has bad reduction at 2? Or does $X$ secretly has good reduction at 2?
What one can be sure is that the closures in $\mathbb{P}^2_{\mathbb{Z}}$ of any such four points cannot be disjoint over $(2)\in{\rm Spec\ }\mathbb{Z}$, since each rational line in $\mathbb{P}^2_{\mathbb{F}_2}$ contains only 3 rational points. If (one of) the cross ratio of the four points is $a/b$ with ${\rm gcd}(a,b)=1$, the same consideration suggests that $X$ has bad reduction at $p$ iff $p\mid a$ or $p\mid b$ or $p\mid(a-b)$.