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

1. Throw an ender pearl through a nether portal
2. Pause the game
3. 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.