Let $\mathcal{C}$ be a category. We can construct a category of morphisms $\mathcal{M}$ by letting the objects be morphisms in $\mathcal{C}$ and morphisms be appropriate pairs of morphisms that give a commutative diagram.
Let $f:A \to B$, $g:C \to D$, $h:E \to F$, and $k:G \to H$. A morphism $(r,s) \in \mathrm{Hom}(f,g)$ consists of a map $r:A \to C$ and a map $s:B \to D$, and a morphism $(t,u) \in \mathrm{Hom}(h,k)$ consists of a map $t:E \to G$ and a map $u:F \to H$, all so that the appropriate diagrams commute.
Part of the requirement of a category is that hom-sets be disjoint. Suppose $(r,s)=(t,u)$ for some $(t,u) \in \mathrm{Hom}(h,k)$. Then we must have $r:E \to G$ and $s:F \to H$, so it must be that $A=E$, $C=G$, $B=F$, and $D=H$.
Since the morphisms $r:A \to C$ and $s:B \to D$ form a commutative diagram with $f:A \to B$ and $g:C \to D$, we have the relations $k \circ r=s \circ h$ and $g \circ r=s \circ f$. I'm not sure how to show from here that $r=t$ and $s=u$, which would show that if two hom-sets are not equal then they are disjoint. I see that they must have the same domain and codomain, but I feel like this isn't enough.
How do we show that hom-sets in a morphism category are disjoint?
You're problem is due to the fact that the correct definition of the arrow-category (of a given category $\mathbf C$) requires that a morphism from $f \colon X \to Y$ and $g \colon Z \to W$, let's call it $\sigma \colon f \to g$, should be a commutative square: a $4$-tuple $\sigma = \langle f,g,k,h\rangle$ with $k \colon X \to Z$ and $h \colon Y \to W$ such that the induced diagrams commute.
The point is that arrow of a category should carry information about its domain and its codomain, and with the definition above every arrow have a unique domain e codomain: it could be possible that there are two $4$-ple $\langle f,g,k,h\rangle$ and $\langle a,b,k,h\rangle$ which are arrows in a category, anyway these are different arrows because they have different source and target (namely $f$ and $g$ in the first case and $a$ and $b$ in the second one).
This is the same problem you have in $\mathbf {Set}$ if you reguard morphism (i.e. functions) as just relations (i.e. subsets of cartesian products): if you consider $f \colon X \to Y$ to simply be a functional relation $f \subseteq X \times Y$ then, if $f$ isn't sujective, it cannot be distingueshed from any other function $f' \subseteq X \times Y'$ obtained restricting the codomain.
Mac Lane solved this problem in the introduction of Categories for working Mathematicians by defining a function $f \colon X \to Y$ to be a triple $\langle X, Y, F\rangle$ where $F \subseteq X \times Y$ is a functional relation.
Hope this helps.