Dear Waqar,
You need to give a different name to each group. Try with this:
<a class="thickbox" rel="my-gallery-[wpv-post-id]" href="[types field="main-picture" raw="true"][/types]">[types field="main-picture" size="thumbnail"][/types]</a> [wpv-for-each field="wpcf-additional-pictures"] <a class="thickbox" rel="my-gallery-[wpv-post-id]" href="[types field="additional-pictures" raw="true"][/types]"></a> [/wpv-for-each]
Notice how I added the post id to make the groups have different names.
Please let me know if you are satisfied with my answer and if I can help you with any other questions you might have.
Regards,
Caridad