Alain.Cochard@unistra.fr writes:

>    * h1
>    foo
>    * h2
>    foo bar
>
> I make the 1st two lines the region.  Then I do
>
>    M-x org-agenda << / foo
>
> and I see
>
>    2 matches for "foo" in buffer: debug.org
> 	 2:foo
> 	 4:foo bar

Thanks for reporting!
Can you try the attached patch?