Your concurrent modification exceptions are coming from removing entries from ArrayLists while iterating over them. Normally you could switch to listIterators instead of iterators, but the doubly nested references cause problems.

The best way to handle this issue is to not remove the objects, but to set them as not active. Then, outside the loop, remove the inactive items. This code can be used to remove inactive items....

universe.removeIf(i -> !i.active);
starships.removeIf(i -> !i.active);
projectiles.removeIf(i -> !i.active);
asteroids.removeIf(i -> !i.active);

You may need to change some of your collision code if you need to concern yourself with colliding with objects that have already become inactive.

@jaLeague Please make sure that our student knows I have created this issue. I will try to get to the school before class ends.