The foot note is not in the TOC. I don't know if this is a bug, or by design.

Created attachment 66922 [details]
Demonstrates footnote not super scripted, and foot note not appearing in TOC.

Attached test case demonstrates the problem with footnote in TOC and reference.

It's hard to say what is bug and what is by design. I don't know if it boils down to the ODT specification, or a matter of a policy decision for LibreOffice.

Anyhow, might be useful to add this document to your test suite such that this scenario gets baselined.

reproducible with LO 3.6.4.3. (Win7 Home, 64bit)

But I think the footnote should not belong to the header, otherwise you would need maybe this footnote also on further pages if the reference text is for instance moved to the next page.  But if you try this in the test document then you will find no footnote on the next page, although you would actually need it in this case.
Therefore, I think the footnote should not belong to the header, but if it should also be mentioned in the reference then it should be superscript and the footnote should also be copied to the page of the reference.  
But I personally would rather say that the footnote should not belong to the header.

When I tested the test document, then it seemed not be possible to format the footnote not as a header.  In addition, I recognised that if I format the header as a normal text body, then the reference will nevertheless be kept and this seems to my mind not to be consistent.

I think this issue needs to be evaluated further and the procedure needs improvements.  Maybe somebody else can help with this issue?

What is mentioned in comment #3 is correct as far as style goes. Refer my comment here:

https://bugs.freedesktop.org/show_bug.cgi?id=47871#c3

I'm focusing on the original report not comment 1 ( it seems like by design btw - who wants a footnote superscript in TOC?)

For description:

I have been able to confirm the issue on:
Version: 4.3 beta1
Platform :Ubuntu 14.04
DE: GNOME3

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As I've been able to confirm this problem I am marking as:

New (confirmed)
Normal - could theoretically prevent professional quality work.
Lowest - seems like a very rare corner case (note not one other person has reported similar problem in 2 years)

Whiteboard Status - NeedsDevEval (might be an easy hack)

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Not present in:
Version: 6.1.0.3
Build ID: libreoffice-6.1.0.3-snap1
CPU threads: 4; OS: Linux 4.15; UI render: default; VCL: gtk3; 
Locale: hu-HU (hu_HU.UTF-8); Calc: group threaded

If I understand the problem well: In the original report the attached document appeared:

Table of Contents
Header 1 paragraph1

Header 1 paragraph1
Here is a reference to the previous paragraph: Header 1 paragraph1

But in LO 6.1 (press F9, refreshing fields):

Table of Contents
Header 1 paragraph

Header 1 paragraph1
Here is a reference to the previous paragraph: Header 1 paragraph

So: The footnote number isn't displayed in TOC and in the reference. So it's formatting is not problem anymore.

In 6.1 and 6.4 master I still see a one at the end. Pasted below:

Here is a reference to the previous paragraph: Header 1 paragraph1

*** Bug 63464 has been marked as a duplicate of this bug. ***

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