Yes, such a family can easily be constructed by transfinite induction. There are only $\mathfrak{c}$ countable unions of closed nowhere dense subsets of $X$; let $(C_\beta)_{\beta<\mathfrak{c}}$ be an enumeration of them. Also, let $f:\mathfrak{c}\to\mathfrak{c}\times\mathfrak{c}$ be a bijection. Now construct a family $(U_\gamma)_{\gamma<\mathfrak{c}}$ by an induction of length $\mathfrak{c}$, where in the $\alpha$th step you choose a new element of $X\setminus C_\beta$ to be in $U_\gamma$, where $f(\alpha)=(\beta,\gamma)$. This is always possible since $X\setminus C_\beta$ has cardinality $\mathfrak{c}$, and you have only chosen $|\alpha|<\mathfrak{c}$ elements so far. In the end, you get a family $(U_\gamma)$ such that each $U_\gamma$ is not contained in any $C_\beta$, and thus has second category.