First of all consider the surface $S=(-3,3)\times\mathbb{R}$. Let $U_1=(-3,-1)\times\mathbb{R}\ \cup\ (1,3)\times\mathbb{R}$ and $U_2=(-2,2)\times\mathbb{R}$. Let the coordinate function on $U_1$ be the identity on the left component, and on the right component send $(x,y)\to(x,-y)$. For $U_2$ use the identity. You can check that this cover satisfies all the conditions in your problem but $S$ is orientable.
If you require $U_1$ and $U_2$ to be connected then it is true (this automatically requires $M$ to be connected). By continuity the transition map for any two charts must have either strictly positive or negative Jacobian in a small neighborhood of any point. So if $M$ is orientable and $U$ is connected coordinate neighborhood, by connectedness $(U,\phi)$ has a well defined orientation.
Suppose $U_1$ in your problem is positively oriented. Then the transition function Jacobian at $W_1$ says that $U_2$ is positively oriented, but the transition function at $W_2$ says the opposite.