The Final Chapter: The Scare in the Score - S12-E7
Other mistake: It is found that the bad guys used Brennan's father's pacemaker to find where the safe house is at. An FBI agent at the scene then states that they "never expected Brennan's father" to be there despite him being the reason they found the place.
Harbingers in a Fountain - S5-E1
Character mistake: Bones gets stabbed with a scalpel and it's sticking out her arm. As a forensic anthropologist she would know the worst thing you can do is pull the item out. Which she does straight away. (00:30:10)
Visible crew/equipment: When Booth checks out of the silver sports car, two yellow tape markers are visible between the two cars. (00:23:35)
The Santa in the Slush - S3-E9
Visible crew/equipment: When the santas ask if Chris is dead, a red tape marker is visible on the floor.
Soccer Mom in the Mini-Van - S3-E2
Continuity mistake: At the end sat on the steps of the Lincoln memorial, Bones' arms keep alternating they way they are crossed. (00:42:30)
Soccer Mom in the Mini-Van - S3-E2
Continuity mistake: Max walks into the meeting room with Bones and the guard closes the door. A few moments later the door is closed again. (00:08:25)
Soccer Mom in the Mini-Van - S3-E2
Visible crew/equipment: When the victim goes back to her car at the start, as she grabs the van door a camera man's hand is reflected in the wing mirror. (00:02:05)
The Glowing Bones in the Old Stone House - S2-E20
Continuity mistake: When Abby is found out, she has her arms waving in desperation in one shot but not in others. (00:38:00)
The Glowing Bones in the Old Stone House - S2-E20
Visible crew/equipment: When Booth is in the kitchen at Carly's talking to the husband who is going over the books of the restaurant, a tape marker is visible. (00:18:30)
The Girl in the Gator - S2-E13
Continuity mistake: The form Booth holds out for Gordon is fully opened. Camera changed and now the form is half folded. (00:06:45)
Continuity mistake: Booth chucks Parker's ice cream on the floor along with the napkin. When Bones picks up the napkin the ice cream has gone. (00:20:00)
Other mistake: Bones produces a gun and states that she got it herself. However it is explained in earlier episodes she is not legally allowed a weapon due to being arrested for shooting a suspect.
Revealing mistake: When Booth is running down the hill, there are marks in front of him from previous takes. (00:36:00)
Revealing mistake: Near the end we see the black FBI vehicle driving over the mine dust and there are tyre marks from previous takes visible. (00:34:20)
Character mistake: Sweets is a psychologist who deals with the team's problems. However he is constantly shown breaking patient confidentiality by mentioning what has been said in sessions.
The Final Chapter: The End in the End - S12-E12
Continuity mistake: When Booth finds Bones she has a piece of glass on her face that turns into 3 pieces then back to 1. (00:03:00)
The Soldier on the Grave - S1-E21
Visible crew/equipment: When Booth leans down to greet Hank, his mic wire is visible against his white shirt under split in his jacket. (00:11:30)
The Final Chapter: The Steal in the Wheels - S12-E9
Revealing mistake: When Booth launches his car off the other car in the derby, the sparks that appear don't line up with where Booth hits the car. (00:35:35)
The Final Chapter: The Steal in the Wheels - S12-E9
Other mistake: When Rolfe walks up to the platform with Angela at the start, he is 3 or 4 steps in front of Angela who swipes her card to grant access to the platform but no alarm sounds. (00:08:00)
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)
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 ★