I'm not sure if this is a bug or an error in my implementation, so I'd appreciate any feedback.

Source HTML:

<ul class="list--experience">
    ...
    <li>Custom child theme and UI plugins, to partition UI enhancements into separate repositories, each with their own documentation, tests and issue tracker <span class="footnote"><a href="https://github.com/dotherightthing/generator-wpdtrt-plugin-boilerplate/wiki/Appendix:-Generated-plugins">DTRT WordPress Plugin Boilerplate Generator: Generated plugins</a></span></li>
    ...
</ul>

Source CSS:

.footnote {
  float: footnote;
  font-size: 8.5pt;
  line-height: 1.64706;
}

section .footnote {
  footnote-style-position: inside;
}

@page {
  counter-reset: footnote;

  @footnote {
    font-size: 8.5pt;
    padding-left: 12px;
    padding-left: 0.75rem;
    margin-left: 25%;
  }
}

Acrobat Pro display:


Acrobat Pro tags:


Acrobat Pro Accessibility Checker output:


Acrobat Pro Accessibility Report:

1. 1-acrobat-pro-display.png‎ 75.7 kB
2. 2-acrobat-pro-tags.png‎ 36.8 kB
3. 3.acrobat-pro-accessibility-checker.png‎ 27.5 kB
4. 4.acrobat-pro-accessibility-report.png‎ 10.8 kB

Hmmm, it looks like a footnote is not allowed within a list item:

1. Screen Shot 2019-09-27 at 10.45.49 PM.png‎ 59.8 kB ‎
   Adobe Acrobat error explanation

This issue is not raised by PAC 3:

1. Screen Shot 2019-09-30 at 5.26.35 PM.png‎ 136.9 kB ‎
   PAC3 Footnote in List

This doesn't have anything to do with list items.
I think the Acrobat accessibility checker is incorrect in assuming that Lbl must have a LI parent. Prince generates an inline footnote as described in the "Tagged PDF Best Practice Guide" which has

<P>
  <Reference>
    <Lbl>
  <Note>
    <Lbl>

Thanks for the clarification. Acrobat has a bug or two, I wouldn't be surprised if they got this wrong too.