File:Wikipedia-logo-v2-fr.svg had a glitch, that has been fixed recently, see this talk.
I compared the two SVG files, and apart from some Inkscape editor settings (btw this file shouldn't contain these metadata), the only change is indeed the removal of the glitch.
Therefore, could you please generate new PNG assets for the following 3 files, that are used by wmf-config/logos.php:
/static/images/project-logos/frwiki.png /static/images/project-logos/frwiki-1.5x.png /static/images/project-logos/frwiki-2x.png
On a related note, you might want to have a look at T358545.