Your fish aren't disappearing, they are "relocating!"

You're seeing the results of some of the fish in your tanks rapidly traveling to the upper left corner of the tank at the exact moment that the new fish hatch. Fish will also "warp" to different places in the tank at various times. This is a phenomenon that has been in every version of Fish Tycoon since the Palm days, and it's a harmless (if annoying) function of how the tank updates are performed.