Let $D$ be an integral domain with fraction field $K$. Let $V$, $W$ be multiplicatively closed subsets of $D$. Consider the rings of fractions $V^{-1}D$ and $W^{-1}D$ as subrings of $K$. Is $(V^{-1}D) \cap (W^{-1}D)$ also a ring of fractions of $D$? That is, does there exist a multiplicative subset $S$ of $D$ such that $(V^{-1}D) \cap (W^{-1}D) = S^{-1}D$?
It seems unlikely, but I am unable to come up with a counterexample.
I don't know the full answer to the question, but here's a partial answer:
I claim (1) is obvious. Here's my proof of (2):
However, I don't know whether your question has a positive answer when $V$, $W$ correspond to infinite unions of primes. An interesting special case would be when $V$, $W$ correspond to (the saturations of) the powers of single elements. That is, is $D_x \cap D_y$ always a ring of fractions of $D$, where $x, y \in D \setminus \{0\}$?