Hmm. I'm seeing that sort of behavior too. If there was a problem with the way Relink interacts with rQT, I'd be happy to fix it, but rQTs behavior is so strange I have trouble believing it's not at fault.
* It lets you create Tiddlers with the same title as pre-existing tiddlers, and it somehow injects them into the story river, even though it's impossible for there to be two tiddlers with the same name.
* It lets you create Tiddlers with an empty name, which is a no-no in Tiddlywiki
* It lets you create Tiddlers with preceding and trailing whitespace characters, which is another no-no.
rQT says it's in beta, so I imagine it may need some more work. Relink works by hijacking the renameTiddler wikimethod. It won't actually touch the "toTiddler" or "fromTiddler", only tiddlers that have the "fromTiddler" somewhere inside them. So if there's a phantom tiddler problem, it's probably in the way rQT is making tiddlers. This may be something to report on their github.