When using the "new" assistant, the inline reference citations always reference what is clearly the wrong reference. Often also using the wrong reference number.
- With the Assistant set to any mode ("Quick", "Research", or "Research (Experimental)")
- Ask any question that will require multiple citations.
- Look at each inline citation reference/footnote in the reply
- Notice that footnote numbered 1 is the only one appearing, and appearing multiple times (usually)
- Notice that after the first footnote numbered 1, it's the wrong reference for the reply context (it should be one of the other references usually)
- If there is a footnote not numbered 1, clicking on it shows a tooltip/pop over that lists the details of reference 1 from the footer.
Example:
Wiht the prompt: "Using Ignition Butane files, can I do a substitution replacement on an existing file /etc/NetworkManager/system-connections/internal.nmconnection to change only line type=ethernet to type=dummy"
Part of the response included this, which is actually the second occurance of the footnote numbered 1.

Looking at the References footer, it's clear that this should have been a footnote numbered 2, and pointing to reference number 2. Following the links confirms this is the case.

I can't consistently replicate the other case where a footnote number may match with the correct reference, but the tooltip/pop over lists the wrong reference link and text.
Footnotes for references are correct for the reply context they're used in, and the tooltip/pop over shows the reference it matches the number for.