I'm trying to solve these two equations: $$\begin{cases} 1-4x(x^2+y^2)=0 \\ 1-4y(x^2+y^2)=0 \end{cases}$$ and I tried to do it by subtracting the first equation from the second, yielding $(4x-4y)(x^2+y^2)=0$. Clearly this is satisfied when $x=y$, which gives $(x,y)=(\frac{1}{2},\frac{1}{2})$, or when $x^2+y^2=0$, which gives $(x,y)=(0,0)$.
But when I plug them back in, it's obvious that $(x,y)=(0,0)$ is not a solution. Where did I go wrong?
You didn't go wrong. Subtracting the equations will preserve any existing solution, but may add others, which aren't solutions to the original equations (as here). So you need to feed the possible answers back into the original equations, as you have done to check that they are valid.