So I want to start by saying that this has been a long-running issue I've been having... I've had to roll back my entire project to a backup at least 3 times due to something similar to this happening and it's very frustrating.
What's happening now is that simply by adding new sprites to a sprite collection, the index breaks in an obvious way, instead displaying part of one sprite and part of another in the scene. In the actual sprite collection editor, the sprite listing appears fine.
I've tried a number of things to fix it to no avail, from recommitting the sprite sheet to Rebuilding Index, to deleting the -tk2d file, even to deleting the sprite sheet texture itself and recommitting. Nothing works.