In the Forest of the Night - S8-E10
Continuity mistake: When Clara mentions worrying about a witch in a gingerbread house while she and the Doctor are searching for Maebh, the phones she is holding switch hands between shots. (00:20:11)
Continuity mistake: During Clara's first conversation with Danny, the folders in her hands are unmarked in close-ups, but have labels on them in wide shots. In addition, the folders and newspaper she's holding keep changing position between shots. (00:07:30 - 00:08:26)
Continuity mistake: When the Doctor shows Clara the "listen" written on one of his blackboards, the handwriting is different to when it was first shown. (00:07:07)
Continuity mistake: The leaf Clara feeds the Old God, which was the catalyst for her parents meeting and which she kept tucked in her book as "page 1", looks completely different to its first appearance in "The Bells of Saint John".
The Bells of Saint John - S7-E8
Continuity mistake: When the Doctor and Clara are sitting at their table on the balcony, talking, the level of Clara's mostly-finished milkshake changes several times, most noticeably when she and the Doctor are arguing over who is going to use her computer to hack the bad guys' systems. (00:31:00)
The Bells of Saint John - S7-E8
Continuity mistake: When the Doctor and Clara, while seated at their table on the balcony, are arguing over who has the better hacking skills while pulling her computer back and forth, in overhead shots their table is somewhere in the middle of the balcony. This contrasts with all other shots, which show their table right next to the railing. (00:31:16)
The Bells of Saint John - S7-E8
Continuity mistake: When the Doctor hands the scone to the waitress, her grip on it changes between shots. (00:33:00)
Continuity mistake: During the sequence involving Rory and Isaac leaving town with the latter disguised as Kahler-Jex in order to distract the Gunslinger so the Doctor can get back to the TARDIS, parked somewhere outside of Mercy, only to find Jex's ship instead, while Amy and Jex wait back at the sheriff's office, the Sun changes position several times, as do the shadows cast as a result. Most noticeably, when the Doctor finds the cable running from Jex's ship to town, the Sun is quite low, as if close to sunset - while appearing high, as if closer to midday, in the scenes of Rory and Isaac distracting the Gunslinger taking place at the same time. During the scenes of the Doctor finding Jex's ship and Amy and Jex in town, it is also earlier in the day. (00:10:50 - 00:17:17)
The Snowmen - S7-E7
Continuity mistake: While confronting Dr. Simeon in an alleyway, when Vastra picks up some snow and remarks about how interesting it is, the fingers of the hand she's holding the snow with change from being extended to curled up and back again between shots. (00:08:58)
Continuity mistake: When Rory finds his dad on the spaceship, Brian is lying on a gurney next to the two farthest slabs, which are empty. When Amy and the Doctor come through the portal to the spaceship, Brian's gurney is between the two closest slabs, with Rory lying on the closest one, which previously had a completely different person lying on it. (00:35:05)
Continuity mistake: When Amy's holding a revolver while arguing with the Doctor, just before she accidentally fires it a second time, she goes from holding it pointed to her right to holding it pointing to the ground in front of her between shots. (00:23:53)
The Wedding of River Song - S6-E14
Continuity mistake: When the Doctor compares Amy's inaccurate drawing of Rory to the real deal and laughs, in a shot facing Rory the Doctor is shown lowering the picture, than in the next shot facing the Doctor he still has the picture raised. In addition, his grip on the paper changes from holding the bottom of the page to the side, and it also switches hands. (00:23:33)
The Wedding of River Song - S6-E14
Continuity mistake: When the Doctor and River are wrapping his bowtie around their hands in a handfasting, the length of the cloth changes between the close-up and the wide shot. (00:37:40)
Continuity mistake: When Alex is hugging George after rescuing him from the peg dolls, George's arms are down in shots facing Alex, but his left arm is up in shots facing him. (00:37:23)
Continuity mistake: When the TARDIS crashes through the ceiling and lands in the tunnel, the side visible to the camera is not the one with the door. The camera cuts away, and when it returns to the TARDIS, on the same angle as before, the door is now facing the camera, as revealed by the sign and St. John's Ambulance medallion. (00:36:16)
Continuity mistake: In the penultimate scene, just before the Doctor melts Amy's Flesh avatar, he points his sonic screwdriver, snapping it to its full length and opening up the four metal bits around the light at the tip. In the next shot, the screwdriver is "closed", but in the shot after that it's "open" again. (00:43:56)
Continuity mistake: The Flesh, the substance that the gangers are made of, is capable of replicating people and their clothing. However, devices such as the sonic screwdriver are off-limits, which is why there is only one even after the Doctor's ganger is created. This is made clear when the Doctor tosses the screwdriver to his ganger before the ganger Doctor sets off to look for Rory. However, when the Doctor, Amy and the three human factory workers are trapped in the crypt with the overheating acid pool, the Doctor is seen using the screwdriver to scan the acid, even though the device should still be in the possession of the other Doctor. (00:28:57)
Continuity mistake: When Idris/the TARDIS stumbles in the junkyard and the Doctor catches her, just before she tells him that one of her kidneys has failed, her right hand, holding a piece of circuitry, moves between in front of his chest in shots facing him and resting on his shoulder in shots facing her. (00:24:48)
The Christmas Invasion - S2-E2
Continuity mistake: After the Sycorax ship has arrived above London, when Rose has decided that they need to shelter in the TARDIS and is explaining this while preparing to put a housecoat/dressing gown/bathrobe on the unconscious Doctor, the garment jumps between the bed and her hands in a few shots. (00:30:25)
The Unicorn and the Wasp - S4-E7
Continuity mistake: Thoughout the episode, Donna's rhinestone-studded hairband changes between going over or under her ears.
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.