So a scene means Shepard doesn't want the tags? I probably would do the same since the Alliance never made any attempt to confirm Shepard's death. Also Shepard is not part of the Alliance anymore. Basically its Shepard way of saying to heck with you Alliance. For her to return them would be a good idea if the dlc isn't completed. She has no right to keep them. She has no idea if Shepard doesn't want the tags or not. Let Shepard decide if he/she wants them.
Well, maybe she didn't have them right at hand in her office on Illium waiting for Shepard to walk right in, and the two don't meet again until the Mars archives in the third game. And when Anderson throws Shepard the tags, assuming it's not new ones, it's within a few weeks at the most of Liara entering the Sol system to study the archives. And Shepard and Anderson greet each other like they haven't talked in a good while. Maybe Liara just passed the tags to Anderson at the first convenient opportunity when it turned out she couldn't visit Shepard personally, and Anderson gave them back the next time he saw him/her - which incidentally happened to be the day the Reapers invaded and he had to spring him/her for active duty.
When you want something personally delivered, even by proxy, and everybody you trust is busy and all over the galaxy, I imagine it can take a while.
Edit: Never mind, redundant post.