I have tiny spheres traveling at a reasonable speed (not fast by any means), and I have a series of static mesh colliders in my world. Sometimes, and seemingly at random, the sphere colliders fly straight through the mesh collider, ignoring it completely.
My question is, is there some way to regulate what happens when a smaller collider finds itself "inside" a larger one, or is there a way to make the physics engine more accurate without sacrificing game performance? It would seem that these small spheres are traveling too fast, and "miss" the boundary of the mesh collider completely, passing right through it and out the other side. How can I prevent this?
You can make the Fixed Timestep interval smaller (Edit->Project Settings->Time). That may help, though maybe not 100% of the time, and it could slow your game down.
Another approach is to have your spheres detect collisions explicitly with code. One way would be by firing a ray in the direction of movement to detect things it is about to hit. Given the distance and velocity you can decide what needs to happen.
A third, "quick-fix" technique I once used was to increase the size of the colliders on my small fast-moving objects. Specifically, the collider was a capsule that started at front edge of my object, and extended backwards well past the back edge. So even if the object travelled through a mesh between frames, the collider "tail" would still hit.
(Not sure I recommend that last approach; there will always be a slow machine or situation that it doesn't catch. Conversely, moving meshes may hit the collider after the bullet-object already passed, leading to a false collision. But I mention it because it may give you ideas, and in my case I was able to tune it to the point where problems were quite rare, and hard to spot when the action was quick.)
The physics engine doesn't really do well with tiny objects, so it's better if you scale the spheres up to 1 unit, and scale everything else to compensate. If it's an issue with the spheres being on one side of a collider during one physics frame and on the other side the next physics frame, so that it's not possible for a collision to register, then increase the physics framerate so this has less chance of happening, or use raycasting like this.