In Chris's campaign, all items collected from Chapter 2 (which is flashbacks from Edonia) appear in Chapter 3. Also in Chapter 2, some certain characters can be killed despite being alive in the next 6 months.
Both Ada Wong and Leon/Helena watched the 'Happy Birthday Ada Wong' tape, yet neither one of them rewound it, and all of them watched it from the beginning.
The chainsaw monster disappears from one area and reappears in the next when Leon and Helena are on the raft.
Leon breaks into a military Humvee to get medical supplies. He does this by breaking a window. Military Humvees invariably have bulletproof windows.
The Player is somehow able to use rifle ammunition in his pistol. Rifle ammunition imparts too much recoil to be used in a pistol.
The grenade launcher fires projectiles hat have a flat trajectory. Grenade launchers fire projectiles in a curved trajectory.
Neither Jake nor Sherry show any signs of growing hair despite being held captivated for 6 months. However, one can conclude that this is the procedure of keeping their general appearances the same.
Jake and Sherry easily retrieve their firearms from a normal-looking locker, including all of their supplies from the past six months. This is highly unusual considering that they are held captive in a place guarded with a high security system (which also has electronic locks) and armed J'avos.
In the underground laboratory, Leon inexplicably empties a sink by turning on the faucet.
Finn blows an entire rail car which must weigh many tons completely off the ground. It would take more explosives than a man could carry to do this.
The aeroplanes that drop paratroopers on the bridge are too low to safely drop paratroopers, not to mention being too slow to fly.
Dead teammates do not have any ammunition on them. There isn't any reason for them to not have ammunition.
The first aircraft carrier has a pit of molten metal aboard. There is no reason for an aircraft carrier to have this.
When shooting at a monster in a cutscene during Jake's campaign, Jake can be heard firing a round, but he cannot be seen shooting at the monster.
Leon kills a zombie with a knife and then leaves the knife within the zombie's head. Although Leon has another knife, it does not make any tactical sense to not keep both knives.
In the banquet hall there are candles burning even though no one could possibly have lit them yet.
In spite of being a mercenary, Jake is only armed with a pistol and no extra ammunition for it at the start of his campaign.
In pursuing Ada Wong, neither Chris nor Piers seem to be aware that she wears totally different clothing from Carla.
Leon is told that there is an elevator leading to a parking garage. Despite this, he later asks how to leave the building and is told this again.
Chris tells Piers to take out 'those' missiles even though there is only one.