Just avoid very small fast moving objects moving towards thin barriers. You can calculate how fast an object steps every tick, it's:
speed x dt
For example an object moving 100 pixels per second at 20 FPS will be stepping
100 x 0.05 = 5 pixels/tick
So if the object is bigger than 5 pixels wide, it will never skip a collision. Even if it was only 3 pixels wide, it could only ever skip a wall that was only 2px thick. So both larger objects and thicker obstacles help prevent the issue.
The C2 engine implements a minimum FPS of 10. So dt never goes above 0.1 - the game goes in to slow-motion at that point.