To Reproduce:

1. Run scene 'BOSS ONE' in the attached project.

2. Notice that after ~140 red bullets are fired collision breaks between some of them and the large white cube.

3. Decreasing the time after which the white cubes are destroyed (shotLife in BulletHell.cs) seems to have an effect on how soon collision breaks, if its 0 red cubes begin flying through the large cube after ~10 shots.

Also it has an effect on the amount of cubes which ignore collision, on 0 nearly no cubes actually collide in the beginning but afterwards its the same as on 10.

4. Remove the line:
Physics.IgnoreCollision(bullet.GetComponent<Collider>(), collider);
from SpawnBullet() in BulletHell.cs (line 54).

Not sure is this exactly what's causing this, but there nothing else in any script in the scene what might effect collision, except a similar statement, on the small red cube which fires the bullets.

Changing the layer to anything else but 'projectiles' seems to have strange effect on the bullet trajectory, they fly into random directions after exiting the large cube instead of going straight.

Collision detection setting seems to have no noticeable effect.