The Future in the Past - S8-E1
Visible crew/equipment: When Bones is on the platform and everyone has gone from the lab, Sweets arrives and we can see a woman walking behind him. There isn't supposed to be anyone at the Jeffersonian except them.
The Secret in the Siege - S8-E24
Visible crew/equipment: When the camera pans to behind Pelant's desk, the camera shadow can be seen on the desk. (00:00:50)
Visible crew/equipment: When we see the aerial shots at the end, the shadow from the filming helicopter can be seen on the ground. (00:39:55)
Visible crew/equipment: At the end we see an aerial shot of the area by the Washington Monument and the shadow of the filming helicopter can be seen on the ground. (00:42:30)

High Treason in the Holiday Season - S11-E8
Visible crew/equipment: While they're doing a full workup of the room at the Riverbanks Inn, just as Hodgins mentions that Ryan Gill has been in the room like an elephant in a china shop, when Agent Aubrey walks in the T-mark can be seen on the carpet. (In the Netflix version the T-mark has been edited out).
The Secret in the Service - S11-E17
Visible crew/equipment: A potential editing oversight can be found as Booth and Brennan are entering the shooting range by watching the space under the rifle of the third shooter. The gas can be seen coming from the spray can to the shooter's right, not the barrel of the rifle. (00:19:05)
The Final Chapter: The Grief and the Girl - S12-E8
Visible crew/equipment: When we see the aerial shot of the harbour in Canada, the filming helicopter's shadow can be seen on the sea surface. (00:13:00)

The Final Chapter: The Steal in the Wheels - S12-E9
Visible crew/equipment: After Fuentes explains to Saroyan why he's not wearing the new lab coat, Fuentes tells Saroyan that he'll be coming to her wedding because they're family, and as the camera pulls back we can see a T-mark on the floor at his feet. (00:18:20)
Answer: Answering my own question here but, having contacted various people involved in the production of Bones including Kathy Reichs, Hart Hanson, Eric Milligan, and Deirdre Lovegood who portrayed Taffet onscreen I finally have the answer. No-one know how she did it due to her constantly working alone. And she never revealed this information before her death.
Ssiscool ★