Given a continuous (Lebesgue) measure preserving map $T$ from a compact convex region to itself that has an aperiodic point (i.e. a point $p$ such that $p \ne T^n(p)$ for any $n$), does the set of aperiodic points necessarily have positive measure?
It can be arbitrarily small as can be seen by taking a rubber disk of radius 1 and gluing the disk of radius $1-\epsilon$ having the same center and turning the outer ring by a small irrational amount (so we are deforming only a small annulus), but can it be zero?
Yes, it can be zero. Take your region for instance to be $D=[0,1]\cup\{1+\frac1n\,:\,n\in\mathbb{N}\}$. Define $T(x)=x$ for $x\in[0,1]$ and $T(1+\frac1n)=1+\frac1{n+1}$. Then clearly $T$ is continuous and measure preserving, and the set of aperiodic points is $\{1+\frac1n\,:\,n\in\mathbb{N}\}$ which has measure zero. I imagine the answer would be different if you also assumed $D$ is connected, but I haven't given that much thought.