This is almost certainly happening to the fish after they die. When a fish dies, the common behaviour of other fish within the aquarium is to eat the body of the deceased fish. Whilst this may sound unpleasant to us, to the fish it is merely a free meal. You'll find that a lot of fish food is made up from other fish (often krill).
The eyes normally go first because they are the most exposed part of the fish and easiest for a hungry fish to eat first. If you have bottom feeders you'll probably find that they will break open the fish and eat the insides (again, to us a little unpleasant but to the fish, fresh meat). "A hungry fish is a healthy fish" - if your fish are not overfed, they will eat anything they can.
Most fish don't have eyelids so it's not a case of the eye lid breaking and releasing the eye to float around the tank.
How to stop the fish dying?
There's actually a bunch of great questions on that right here on this site so check some of those out for a detailed answer:
* An answer by me is on these questions
The best way to ensure the health of your fish is good though is with clean water and consistency.