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I ran into this issue today (Fish 2.7.1), and was ready to file a new issue report when I found this one. Here's an asciicast:
This can cause a surprising behavior when interacting with a file named ~<your username> and selecting it using tab completion. Since the ~ is not escaped, the resulting command will reference ~<your username> which Fish helpfully expands to your home directory.
Notice that the tilde is actually escaped in the list of completion suggestions before selecting one, oddly enough.