I have two independent variables $X$ and $Y$.
$W=X-Y$ when $X\sim \mbox{Bernoulli}\left(1/2\right)$ and $Y\sim N(0,1)$. This puts $\operatorname{Var}(x)=1/4$ and $\operatorname{Var}(Y)=1$, but I have to be misunderstanding something because if $\operatorname{Var}(W)=\operatorname{Var}(X)-\operatorname{Var}(Y)$ then the $\operatorname{Var}(W)$ is negative, which makes no sense.
What am I missing?
The thing you are misunderstanding is that $\operatorname{Var}(X-Y)\not=\operatorname{Var}(X)-\operatorname{Var}(Y)$.
The accurate formula is $\operatorname{Var}(W)=\operatorname{Var}(X-Y)=\operatorname{Var}(X)+\operatorname{Var}(Y)$.