Here is an alternative to Count Dracula's (correct) argument that emphasizes instead the constancy of the Hilbert polynomial for a flat family of projective schemes.

As above, assume that $Y$ is a DVR. For one fixed irreducible component $Z_{\eta}$ of $X_\eta$ of minimal dimension $d$, denote by $Z$ the Zariski closure of $Z_{\eta}$ in $X$ together with its closed immersion $u:Z\to X$. Denote by $W_{\eta}$ the union of all other irreducible components of $X_{\eta}$, and denote by $v:W\to X$ the closure of $W_\eta$ in $X$. By construction, both $Z$ and $W$ are flat over $Y$, since every associated point is a generic point of $Z_\eta$, resp. $W_\eta$.

The closed immersion $u$ and $v$ determine an associated morphism of $\mathcal{O}_X$-modules, $$(u^\#, v^\#):\mathcal{O}_X \to u_*\mathcal{O}_Z \oplus v_*\mathcal{O}_W.$$ The restriction of $(u^\#,v^\#)$ on $X_\eta$ is injective. Thus the kernel of $(u^\#,v^\#)$ is a subsheaf of $\mathcal{O}_X$ that is torsion for $\mathcal{O}_Y$. Since $\mathcal{O}_X$ is flat over $\mathcal{O}_Y$, the kernel of $(u^\#,v^\#)$ is the zero sheaf.

Denote the quotient of $(u^\#,v^\#)$ by $\mathcal{Q}$. The restriction of $\mathcal{Q}$ on $X_\eta$ has support whose dimension is strictly smaller than the dimension of any irreducible component of $X_\eta$. In particular, the Hilbert polynomial of $\mathcal{O}_{X_\eta}$ agrees with the Hilbert polynomial of $\mathcal{O}_{Z_\eta}\oplus \mathcal{O}_{W_\eta}$ modulo the subspace of numerical polynomials of degree strictly less than $d = \text{dim}(Z_\eta)$.

Now consider the restriction $(u_0^\#,v_0^\#)$ of $(u^\#,v^\#)$ to the closed fiber $X_0$. By the flatness hypothesis, the Hilbert polynomials of the domain and target of this homomorphism equal the Hilbert polynomials on the generic fiber. Thus the difference of these Hilbert polynomials on $X_0$ equals the difference of these polynomials on $X_\eta$, and we know that this difference is a polynomial of degree strictly less than $d$. The cokernel of $(u_0^\#,v_0^\#)$ equals the restriction $\mathcal{Q}_0$. If the induced morphism $\mathcal{O}_{Z_0}\to \mathcal{Q}_0$ is nonzero at some generic point of $Z_0$, then the support of $\mathcal{Q}_0$ has an irreducible component of dimension $\geq d$. Thus the Hilbert polynomial of $\mathcal{Q}_0$ has degree $\geq d$. Since the difference polynomial has degree strictly less than $d$, the kernel of $(u_0^\#,v_0^\#)$ has Hilbert polynomial of degree $\geq d$ counterbalancing the Hilbert polynomial of $\mathcal{Q}_0$. In particular, the kernel of $(u_0^\#,v_0^\#)$ is not zero.

By the flatness hypothesis, every associated point of $X$ is contained in $X_\eta$. Thus, every generic point $\xi$ of $X_0$ is the specialization of a generic point that is either in $Z$ or in $W$. Thus the localization $\mathcal{O}_{X_0,\xi}$ either factors through $\mathcal{O}_{Z_0,\xi}$ or factors through $\mathcal{O}_{W,\xi}$. Therefore the kernel of $(u_0^\#,v_0^\#)$ is in the kernel of the localization at every generic point of $X_0$. Since the kernel is nonzero, $X_0$ has embedded associated points, contradicting the hypothesis that $X_0$ is geometrically reduced. Therefore, by way of contradiction, the support of $\mathcal{Q}_0$ does not contain $Z_0$. So $Z_0$ is not contained in $W_0$.

Now we continue by induction on the number of irreducible components, replacing $X$ by $W$.

actual fiberin the sense of EGA IV$_2$ 4.7.12 (also see 4.7.4ff). Hence, IV$_3$ 12.2.4(ix) [real content is 12.2.1(xi)!] gives the result without projective methods (i.e., no Hilbert polynomials). $\endgroup$ – nfdc23 Dec 9 '15 at 1:52