The colonists in "Power of the Daleks". Daleks have conquered the Earth twice! Now there are three on a derelict ship. You'd Expect: The colonists would read their history and act accordingly. Even if we accept that the story is set before "The Daleks' Master Plan" and ignore the invasions in "Doomsday" and "The Stolen Earth"/"Journey's End" (which weren't written for another four decades), you'd think they'd at least remember the Dalek invasion of Earth in the story called "The Dalek Invasion of Earth." Instead: They accept these supposed servants at face value. This leads directly to the Daleks manufacturing dozens more, and exterminating around half of the colonists
In "Invasion of the Dinosaurs" episode 3, Sarah Jane decides to take pictures of a chained, sedated Tyrannosaurus Rex. You'd Expect: Her to keep pictures to a minimum, not use flashes or anything that could annoy the dinosaur, and keep to the small antechamber of the main hanger where the dinosaur is held. Instead: She jams on that flash hard as hell, and even when the dinosaur stirs, she just waltzes in to take close-ups, naturally awakening the dinosaur, which breaks the chains, because The Mole has tampered with them. She's hit by a falling 2x4 while screamingly trying to open the exit door, which has been locked by The Mole, as the dinosaur bashes the anteroom with its tail. Thankfully, Sarah Jane's Character Development moves her far away from these hapless moments as she gets older.
In "The Sea Devils", the Royal Navy has rescued both The Doctor and The Master from their watery prison just in time, and have The Master under guard in a hovercraft. You'd Expect: The Royal Navy to keep a massive armed guard on The Master, ready to fill him full of lead whether The Doctor likes it or not. And, The Doctor might warn them about his mastery of disguise. Oh, and you think the crew of the hovercraft might keep an accurate count of their own members. AND, if that weren't enough, that they would always make sure more than one person is guarding a piece of military equipment on the order of a hovercraft. Instead: The Master is apparently left by himself with one sailor to guard him on a small hovercraft. He somehow has time to hypnotize the salor, place a Perfect Latex Disguise on him and palm him off as The Master's own corpse. Then, as The Doctor and the Royal Navy troops are gawking at the reveal, The Master makes off with the hovercraft. This was the serial that the Royal Navy chose, out of all Doctor Who, to endorse and lend the BBC resources for.
At the end of "The Deadly Assassin" serial, after the Doctor leaves in his TARDIS, the two Time Lords he has befriended witness the Master closing the door to his own TARDIS, proving that he isn't so dead after all. You'd Expect: them to at least try to apprehend the Master — if not directly, then by informing the proper authorities. Even if they didn't succeed in getting him, at least they made an effort. Instead: not only do they do nothing, they take the time to speculate whether the Doctor will ever encounter the Master again, as the villain escapes right in front of them.
Rose in "The Empty Child". A rope swings in front of her in WWII London and she holds onto it. Then it starts moving away. You'd Expect: She would let go of it. Instead: She holds onto it as it pulls her of the roof and is left dangling from a great height.
In "The Girl in the Fireplace", at the end, the Doctor wants Reinette to come with him. However, the time window into her time forces her to take "the slow path" to his next visit. You'd Expect: He'd either bring her through the time window to avoid the problem, or he would use the TARDIS to get her. Instead: He tells her she has two minutes. Two minutes later, he goes back through the time window, but it's been several years in her time, and she's dead by the time he shows up.
In "Evolution of the Daleks", two Daleks take a platoon of Dalek-controlled humans to destroy the Doctor. When the time comes to actually do so however, it's revealed that the Dalek's control of the humans is a bit faulty, and the humans promptly turn on their masters. You'd Expect: The Dalek commander (who was remotely monitoring the situation) to immediately realise that the humans are out of their control, and activate the self-termination devices placed in their bodies as a precaution. Once that's done, the Daleks accompanying them can exterminate the Doctor themselves. Instead: The humans are allowed to carry on shooting at the Daleks for a full minute, and succeed in destroying both of them. It's only after their destruction that the Dalek commander decides to terminate the humans.
Davros criticizes the Doctor for letting people around him die on his behalf, accusing him of turning people into weapons and even comparing it to his own creation of the Daleks. You'd Expect: The Doctor would laugh at Davros's ridiculous logic, pointing out that he's never told anyone to commit suicide for him and all those people acted of their own free will, whereas Davros created the Daleks specifically to kill people and is currently planning to wipe out the entire Universe. Instead: The Doctor believes every word and is convinced that he truly is a monster for just trying to do the right thing.
"The End of Time, Part 2":
Rassilon arrives on Earth via a temporal link set up by the Master, which will soon bring the Time Lord homeworld Gallifrey back into existence. The Doctor doesn't want to let this happen, and threatens to shoot Rassilon with a revolver. Rassilon holds off on doing anything, and then the Doctor wheels around and points his gun at the Master, the death of whom would also prevent Rassilon's plan from working. You'd Expect: Rassilon to take full advantage of the Doctor's back being turned, and to blow the Doctor into his component atoms (which we'd seen Rassilon do to a rebellious Time Lady earlier in the episode). Instead: Rassilon just stands around and does nothing, eventually giving the Doctor time to Take a Third Option and disrupt Rassilon's plan without killing either him or the Master.
Rassilon still has the advantage and it's only a matter of time until his plan succeeds as long as he keeps the Master alive and on side. The Master is somewhat miffed that his own plans have blown up in his face, but is nonetheless willing to join Rassilon and the Time Lords in their ascension. You'd Expect: Rassilon to humor the Master and tell him what he wants to hear long enough for him to keep the Doctor from foiling his plan and then dispose of him when convenient. Instead: Rassilon immediately rejects the Master, saying "You're diseased!" and explaining how he could never join them. This infuriates the Master, who attacks Rassilon and provides the Doctor with the distraction he needs.
The Doctor and the group he's stuck with have managed to capture a member of the reptilian race, the Silurians, that have abducted several humans. He wants to use the Silurian as a hostage to get a prisoner exchange and needs her unharmed. Among those with him are a woman whose husband and son have been abducted, as well as the woman's father who has been poisoned by a Silurian attack. The Doctor is planning on going underground to negotiate with the Silurians. You'd Expect: The Doctor, having interacted with humans for so long and knowing that they are emotional, would keep the woman and her father with him so that they can't go Mama Bear or Papa Wolf on the Silurian, with the consequences that would entail. Instead: He leaves these two as part of the group guarding the Silurian, and the woman conducts a violent interrogation on her.
Also when Ambrose tasers Alaya... You'd Expect: Ambrose to simply leave Alaya alone after that, considering how remorseful she was. She also knew full well that Alaya was a Death Seeker who wanted her own death to spark a war between humans and Silurians. Instead: Ambrose, after being taunted by Alaya, electrocutes her to death which worsens Human/Silurian relations.