There's a loyal, honorable knight named Eldigan who is best friends with Sigurd and vassal of King Chagall. Chagall is meanwhile in league with the Big Bad and murdered his father to ascend the throne. After dismissing his sister's concerns over this, Eldigan tries to talk Chagall into not attacking Sigurd and is thrown into the dungeon for his trouble until Sigurd rescues him. You'd expect Eldigan to renounce his knighthood and not fight for a king who attacked his sister and fiefdom, maybe even join Sigurd's army. Instead he insists that his honor as a knight comes first, rescues him from Sigurd, and then attacks Sigurd on Chagall's orders a while later. He can be persuaded to stop by Raquesis... in which case he rides back to try talking Chagall out of attacking Sigurd again. Chagall immediately orders him executed in this case. Even Worse in the Oosawa manga adaptation when the Agustrian knight Zyne tells him in no uncertain terms that Chagall will execute him and that Chagall is being brutal to the people, who would definitely prefer Eldigan to be their king. Eldigan refuses and continues to refuse after Sigurd tells him to honor Zyne's dying wish. Admittedly, he is ashamed of his incestuous feelings for his sister in the manga and those would pose a HUGE problem if he became the King, but even running away to live as a hermit would be smarter than being loyal to Chagall.
In Chapter 3, Roy turns up at Araphen with a small amount of plucky but low-level fighters (and a really old Paladin) while Narcian, King Zephiel, and Idoun (the Final Boss) are still there. The King and his forces have just finished sacking the place to squash the Lycian Alliance. You'd Expect: That Zephiel would at least want to know who was leading the pathetic remnants of the Lycians and, once he found out, to squash them personally. He's more than capable himself even if he didn't have a bunch of manaketes with him at that moment. Instead: He doesn't bother and dismisses Idoun's suggestion to fry them and leaves with her. To his credit, he does order Narcian to take care of it, and as a dragon general Narcian would tear them apart easily. But... Narcian hands the job to a knight (who Roy's company is capable of defeating) so he can go leer at Clarine.
King Fado gave his children Eirika and Ephraim bracelets that function as a twin key to the nation's Sacred Stone, a powerful artifact that is one part of a seal on the Demon King. He entrusts the knight Seth with the secret and orders him to escape with Eirika when Grado invades. While on the run, a thief nabs the bracelet and Seth insists that they go take it back. You'd expect: That after reclaiming it, Seth would tell Eirika what it is so that she knows just how important it is to keep it safe. Instead: He tells her that it is very important, but decides that this does not fall under the heading of "the right time" (what Fado had told him about when to reveal the secret) and refuses to say why it is very important. As such, she decides that even a very important royal bracelet isn't worth allowing hostages to be eaten by giant spiders and hands it over to the dark mage that demands it... and then Seth tells her, after it's in enemy hands. It's just a good thing that they had enough badasses to take it back.
When the mercenaries meet Lethe and Mordecai for the first time, Soren immediately insults them as sub-humans. Mordecai is, of course, pissed. You'd expect: Seeing a man Mordecai's size getting angry, Soren would realize he'd gone too far and back off. Instead: He keeps taking potshots at him until Mordecai attacks him, causing Ike to have to rush in and rescue him. Furthermore: When Ike gets hurt, Soren tries to attack Mordecai with wind magic until Ike pulls him back, only apologizing when Ike scolds him for going too far.
Early on, one of the first main antagonists, a Begnion soldier Jarod, is desperately trying to shut down the Dawn Brigade, as they are what could potentially lead Daein into overthrowing Begnion. After the first chapter introducing the Dawn Brigade, his soliders chase them through the streets and Micaiah showcases her healing powers to save a dying boy, which require her to sacrifice her own health. You'd expect: Micaiah expends her life energy here, or gets captured by the soldiers. Instead: They escape unharmed, and the soldiers stand around and do nothing about it, despite that a moment ago they were willing to kill an innocent child just to get at her.
Also, early on in the story, Micaiah, the one Jarod is after, abandons her team to buy time for them, running into Jarod. You'd Think: Jarod would cut her down where she stands, as he'd been planning to do the entire time. Instead: He sends her to jail, where she meets up with the traders from the previous game, and Kurth. Nice Job Fixing It, Villain.
After Micaiah is made general of the Daein army, she leads an all out assault on the Empress's army instead culminating in an assassination attempt on the Empress herself. However, this fails spectacularly, and Sothe gets captured and nearly dropped to his death because she refused to stop the assassination attempt. You'd Expect: Micaiah is captured by Sanaki's army, or she at least explains that Pelleas is under a blood pact with Lekain. Instead: She panics, Tibarn lets Sothe go and the all-out bloodbath continues until the situation reaches critical mass and Ashera goes berserk and turns all the NPCs into stone.
Prior to the beginning of the third level, Chapter 2: "Sheperds", the player character gets introduced to Chrom's millitia, The Shepherds. During that scene, Vaike goes "Can he/she do this?" and lets out a burp, which The Avatar character doesn't mind (and is rather amused)... but Maribelle, the local Troubadour (healer mounted on a horse), is so repulsed by Vaike and the Avatar that she leaves the Shepards' Garrison room in a huff before even Chrom returns to deliver the news of the voluntary expedition to Regna Ferox to set up an alliance with them to counter the problems with Plegia and the zombie creatures called Risen. You'd Expect: That after Chrom delivered the news about the expedition to everybody in the room, Vaike, Lissa, Chrom himself, or one of the other Shepherds would go look for for Maribelle, who left the room earlier in a huff, and tell her about the mission to Regena Ferox and invite her to join them. It's always good to have a backup healer in case there's the off-chance the main healer (Lissa) falls in battle on the way there. If they had a back up healer, they wouldn't be expending vulneraries. Instead: They completely forget about Maribelle. And she never even hears about the expedition to catch up with the rest of the Shepherds (unlike Stahl, one of of the cavaliers, and Miriel, the mage, who were among the last to hear about this expedition). The Result: Maribelle is left behind in Ylisse, and when Plegian troops attacked Themis, another area in Ylisse, she gets kidnapped by the Plegians and falsely accused to being a spy, which gives Gangrel, the king of Plegia, who has been looking for excuses to start a war, a very convenient excuse to start pointing his fingers at the Ylisseans, causing the Ylissean-Plegian War to start very quickly, which in turn, leads to the suicide spoilers unless you play one of the Spot-Pass exclusive missions unlocked after clearing Chapter 25 of Emmeryn, the exault of Ylisse.