The bug
Throwing ender pearls through portals will print the aforementioned message to the log twice for each ender pearl once the game is paused, and possibly also on autosaves. These appear to build up indefinitely, and this count will only reset once the world is exited.
How to reproduce
Throw an ender pearl through a nether portal
Pause the game
Check the console output
Expected results
There would be no error messages.
Actual results
There is evidently some issue happening behind the scenes with ender pearls.
Can confirm.