In polar coordinates, the origin has $r = 0$, but $\theta$ is not unique.
what sort of problems does this create, and how can I resolve them? For example, suppose an ant is wandering around a plane. Its speed is
$$s = \sqrt{\dot{r}^2 + r^2 \dot{\theta}^2}$$
but if the ant wanders through the origin a quantity like $\dot{\theta}$ is undefined. In this particular case I can deal with it because the limit
$$\lim_{r\to 0}\ r^2\dot{\theta}^2$$
is defined. Similarly, if I want to find an area with integration, I'd need to look at the Jacobian
$$\left|\begin{array}{cc}\partial r / \partial x & \partial r / \partial y \\ \partial \theta / \partial x & \partial \theta / \partial y\end{array}\right|$$
which is not defined at the origin. Again I can get around it. If I want the area of the unit circle, for example, I can take
$$\lim_{\epsilon \to 0} \int_{\theta = 0}^{2\pi}\int_{r=\epsilon}^1 r\ \textrm{d}r\textrm{d}\theta$$
How do I know I can always work around things like this? If I receive some other coordinate system, how can I tell if the points with no unique coordinates are going to give me trouble?
For integrals you can generally ignore stuff like this. This is because integrals ignore what's happening on a set of measure zero, so as long as the part of the thing you're integrating over where $r = 0$ has measure zero, you can just ignore that part. For example, if you're trying to figure out something about a particle involving an integral, and the set of times that particle is at the origin has measure zero, you're fine.