Let $f(x)=x-y$. Then $$\frac{\partial f}{\partial x}=\lim_{h\to 0}\frac{f(x+h)-f(x)}{h}=\frac{x+h-y_h-x+y}{h}=\lim_{h\to 0}\frac{h+y-y_h}{h},$$ noting that $y$ can depend on $x$ (that's why I wrote $y_h$).
Now if instead we let $f(x,y)=x-y$, then $$\frac{\partial f}{\partial x}=\lim_{h\to 0}\frac{f(x+h,y)-f(x,y)}{h}=\lim_{h\to 0}\frac{x+h-y-x+y}{h}=1$$ which is, in general, not equivalent the first result.
Does this mean that $\frac{\partial}{\partial x}(x-y)$ is an ill-defined expression?
The only way in which $\frac{\partial}{\partial x}(x-y)$ is ill-defined, is the same way in which the function $x-y$ is ill-defined. That is, the very instant we define the function $x-y$, its partials are also well-defined.
For instance:
How we define $\frac{\partial}{\partial x} (x-y)$ itself will be context-dependent.