Which markers did you use? It is hard to judge without understaning the protocol, but I imagine these cells were quickly recognised by the mice immune sistem as well as interacted with native proteins...

My marker is CD45. Not only in my data, it appears in others' published data as well. I think the antibodies are not the problem. The double positive cells appear in BM,pbmc,spleen and liver. 

CD45 should not be crossed with human and murine.  You can double check with the antibody. Aonther reason maybe the cells may dying or sticky. You can add DAPI before flow to gate out the dead cells. 

Why CD45 not cross with human and murine? Double positive cells can be found in others' papers as well.