They Keep Killing Suzie - S1-E8
Visible crew/equipment: When Owen responds to Susie talking through the computer monitor and says "you frighten the s**t out of me" a boom mic drops into shot above his head.
End Of Days - S1-E13
Visible crew/equipment: After Lisa appears to Ianto in the holding area, she disappears, when the camera changes angles you can still see her standing in the corner of the room on the right side of the screen. (00:12:50)
Answer: He might have requisitioned or stolen it from Torchwood London, or he might have been ready down below once it'd been severed, searching for "the right Doctor" and not knowing that the newly-regenerated Doctor was the one he was looking for.
Captain Defenestrator