Well, when it shows Jean talking to the lady who was asking about Marco, it shows a headless person on the roof. So I believe that was Mina. The person Annie was apologizing to was not Mina. Of course, it wasn't Marco either since he was bitten into. She could've even just have been apologizing to a random dead person.
If you read the manga, it does show how Reiner was forcing Annie to take of Marco's gear. Reiner, Bertl, and Annie were each saddened about Marco's death.
Even so, maybe Annie was apologizing to Marco. Reiner probably wanted her to take the body and dispose of it herself. She knew Jean would come by, knowing they were friends, so she propped it against a wall instead. That is my personal belief.
Annie has feelings too. It shows her crying over Marco in the Manga. Of course, she would do something like this to make sure Jean would know about Marco's death.
