I think that the police may have tracked Meredith's blood into Filomena's room. I see no evidence that they changed shoe covers going from one room to another, as I have watched the Oggi-hosted videos. However, luminol-positive spots are only presumptive blood, and these tested negative by TMB (and there is no record of confirmatory testing). Amanda's DNA might have been present in either the hall or in Filomena's room; if the former, it could have been tracked in on the shoes of the forensic police.
Or to put it even more simply, how do we know traces weren't tracked in during the chaos on the afternoon after the murder? Anyone could have stepped on Rudy's bloody shoeprints. At a minimum we know Filomena was allowed to enter her room, move stuff around and do preliminary forensic analysis of 'glass on top of clothes'. Only Meredith's room was secured before the investigation began.