Whenever a project_id is involved, the value 0 is used to indicate "all projects" (for example when filtering bugs). So, when checking for all categories of a project, the query should check "project_id = <requested value> or project_value = 0".
However, in the category_api.php file, line 565, the function category_get_id_by_name() only checks for the project_id given in parameter, which triggers an error (or returns false) when the function is called on a category common to all projects, despite being logically available.

It can be avoided by a call along these lines:
$id = category_get_id_by_name($name, $project_id, false);
if (!$id) {
$id = category_get_id_by_name($name, 0);
}

But I believe this isn't the intended behaviour.