Why is hook_menu_local_tasks_alter called twice?
If you are familiar with the command line, you can use the following command to return file names and line numbers where this hook is being called.

For example, change directories into your /sites/all/modules directory or other module directory and run,

(assuming your are using mac or linux)

$grep "menu_local_tasks" * -rn


or as Clive has it below.

$grep "drupal_alter(\'menu_local_tasks\'" * -rn


*Note, the backslashes escape the single quotes.

Jason.