I think the problem with the shoe is being found outside by Greta's crew. The shoe was completely missed...which I find terribly odd being they had the bonfires, parties, and other things going on in their backyard after Maria was murdered. It was overlooked by Cesar, Christina, AND all of the LE scouring that yard and home for clues to this horrific murder. How did it go unnoticed by all those people for a month or so?!
However, we don't know if they took the other shoe found in the garage in as evidence...do we? I have forgotten if we have a complete inventory of what they recovered as evidence. If the shoe outside did have blood on it from Maria, I would assume the other shoe still inside the garage could have blood on it, too.
I don't think they are Maria's. I don't see her kicking off her shoes as she was being fatally hit in the head and having her throat cut after her death. There would have been blood on both shoes from her wounds and from pooling of blood around her.
Besides, if they were determined to be Maria's...Wouldn't they be considered more important to the case than "might be used by the DA"?