https://github.com/jenkinsci/jenkins/pull/10245 modernized the Jenkins header. It adds the class "jenkins-avatar" to all icons in the header, thereby having them all overlayed with a circular mask. Custom icons can have a square shape and are wrongly cut by that circular mask.

For reproduction install a plugin with custom global actions (most simple: sidebar plugin, which can add arbitrary custom global actions).

Be aware that screenshot is with custom header plugin installed, but custom header plugin does not cause this (clarified in https://github.com/jenkinsci/customizable-header-plugin/issues/215)

The relevant line is probably https://github.com/jenkinsci/jenkins/blob/60df85549929c6e1e75eb134fff933412a8249ac/core/src/main/resources/lib/layout/header/actions.jelly#L49

I could create a PR to simply remove the class attribute but I'm not sure if I can easily test this locally, given I'm behind a company proxy that interferes with the maven build.