This is a problem with triangulation.

Three.js uses a fork of earcut. Looking at the open issues, there are a few similar problems. In particular, earcut does not seem to like when a contour crosses itself and forms a hole next to the edge:

(image source)

Based on this information, I hypothesized that my arcs might be overlapping slightly and crossing each other at intersection. This way, holes/loops would form, completed by the lines automatically added by Three.js. To test this theory, I shortened each arc by 0.001 radians and the glitch disappeared.