I still don't know exactly how they got created, but I have entities that show up in my sidebar on one of my maps. I think it happened after I dropped in terrain with MCEdit, because the entities copied into the world weren't killed by the /kill @e[type=!Player] command (but were killed by MCEdit's entity delete feature) but it is more likely related to FallingSand that fell into the void, because the "ghost" entities have scoreboard values that correspond with an experiment I was running.
In this screenshot, there are no entities alive other than the player. I've used the /kill command probably dozens of times since they appeared. I've tried using MCEDit's Kill Entities feature, and it does nothing, but then again, it doesn't select under the void, contributing to the idea that perhaps there's a memory leak of entities under it.
You need to use
/scoreboard players reset * [objective]to remove all records (or optionally only records for a certain objective). The game is assuming the names there are just fake player names (which is a usable feature) since, as you've observed, no entity was destroyed in-game because you used a third-party editor to avoid the function of removing scores from an entity that was being tracked.