I decided to make an Ocean Monument my base of operations and used glass for the "entrance" and above my bedroom. The Cod and Salmon that tend to go too close to the Glass start to freak out. They spin around in circles as if trying to go through the glass. It only seems to happen when they are above the glass. I have a glass encased staircase that they don't have any troubles around. They don't all get stuck but they only get unstuck if another mob pushes them or they die.