Facing an issue where some of the legend icons like 'closed', 'opened', 'project', 'edit' etc. on the events are missing in the thread timeline.
Seems to be affecting both issues and pull requests.
With the extension enabled:

With the extension disabled:

Sample thread: https://github.com/freeCodeCamp/freeCodeCamp/pull/36808
This is intentional.
https://github.com/sindresorhus/refined-github/blob/eca0a5319db1f77bb252fe7c9fe71a98dc26e6da/source/features/deemphasize-unrelated-commit-references.css
You can override that style in the extension if you prefer to see them:
.TimelineItem:not(.TimelineItem--condensed) ~ .TimelineItem .TimelineItem-badge {
visibility: unset;
}
deemphasize-unrelated-commit-references should not hide those icons, but just the icons of commits that don't belong to the current PR.

To fix this specific problem we can change the selector to only hide the commit icon:
.TimelineItem:not(.TimelineItem--condensed) ~ .TimelineItem .TimelineItem-badge .octicon-git-commit {
display: none;
}
However it would leave a white gap:

If anyone wants to help, here's a testing link:
https://github.com/sindresorhus/refined-github/pull/2415#ref-commit-16050d5
Perhaps this cannot be solved with CSS alone.
I implemented the fix suggested above because this was an ugly bug.
The bug now is reduced to:

To fix that, the feature needs to be re-implemented via JavaScript, sadly.
I think we can leave it as is until someone opens an issue for that.