Problem
When working on a project with multiple git repositories, the Git Pull option has the wrong repository pre-selected. Open Commit tool window, group the view by Repository, select one of the repositories > right-click > Git > Pull..
The Pull to dialog is prepopulated with a repository that is not selected.
Resolution
Disable the option - Settings (⌘ + , or Ctrl + Alt + S) > Version Control > Git > Execute Branch Operations on All Roots?
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