Do you have a cover over your filter?
On my Hydroscope 12, the filter had a hole just big enough to suck up dwarf shrimp, baby platies, and yes....even eyes.
I had a pleco one day and as I happened to be watchin, he swam right up to the pump, and got his head stuck inside!
I panicked, turned the filter off, and saved him, but he lost and eye from the incident.
He lived another month and a half just fine after that, until one day I came home from work and he was stuck in there again (thought he woulda learned but...)
If this is indeed your problem...easy fix.
Go to Pay-less, or somewhere and just grab one of their free 'lady stockings' that women use to try on shoes with (preferably not used yet...).
Take it back, and stretch it out around the pump, and secure it with a rubber band and your all set!