Screenshot attached, for Refined GitHub disabled and enabled. The search box is huge on issues pages.
Refined GitHub disabled:

Refined GitHub enabled:

(Pull requests page as well)
The error boils down to the rules in source/features/widen-search-field.css@6cc38da#L1-L10 which were added 5 months ago, so this might be caused by a CSS change on GitHub's end.
Quick and dirty workaround (which disables the automatic expansion of the search field, though):
.subnav,
.subnav-search,
.subnav-search-input,
.subnav [role='search'],
.page-content .subnav > .float-right { /* Global search field container */
flex-grow: unset !important;
display: unset !important;
}
A proper fix is far beyond my CSS skillset :-)
It would be cool, to have even CSS features listed on the options menu so they can be easily disabled.
https://github.com/sindresorhus/refined-github/blob/24b52f9c72068fc9368e6cf58e8d758168e89011/source/content.ts#L4-L18
But for now, I added the CSS from @rfc1459 in the options menu. Thanks!
Most helpful comment
It would be cool, to have even CSS features listed on the options menu so they can be easily disabled.
https://github.com/sindresorhus/refined-github/blob/24b52f9c72068fc9368e6cf58e8d758168e89011/source/content.ts#L4-L18
But for now, I added the CSS from @rfc1459 in the options menu. Thanks!