I've heard of pieces of plastic floating around in the tanks; these are pieces left over from molding of the tank or trailer construction. Some are small but not small enough to be sucked up by the pump others are large (openings for hoses, fill pipe, vent ...etc. These pieces as the tank empties can block the pickup line then when you fill they float away from the pickup line.
The only way to fix this would be to access the tank, try to remove the debris or change the pickup end so it's like basket with multiple openings.