I'm reading this paper on arxiv link.
So far OK.
Now this I don't understand. Take $s=\frac 12$. They say that by density the operator $(-\Delta)^s$ is defined on $\mathbb{H}^s(\Omega)$. Then they say that the theory of Hilbert scales shows that the domain of $(-\Delta)^s$ is $H^1_0(\Omega)$. But in the very next line they claim that $\mathbb{H}^s(\Omega)= H^{\frac 12}_{00}(\Omega)$, which is not $H^1_0(\Omega)$. What do I miss?


I think the authors are somewhat inconsistent in what they mean by the domain of an operator. Let's ignore the boundary conditions for now and focus on the order of smoothness.
When they say that by density, $(-\Delta)^s$ can be extended to $\mathbb{H}^s$, this means as an operator from $\mathbb{H}^s$ to $(\mathbb{H}^s)'$. Indeed, you can see this from the definition of $\mathbb{H}^s$: if $u=\sum u_k \varphi_k$ then $(-\Delta)^su = \sum u_k \lambda_k^s\varphi_k$ which is not generally in $L^2$ since $\sum |u_k|^2\lambda_k^{2s}$ need not be finite.
An operator that maps $\mathbb{H}^s$ into $L^2$ is $(-\Delta)^{s/2}$. When they write $\operatorname{Dom}(-\Delta)^{s/2}$, the mean as an operator into $L^2$.
Summary: