Logically hitting someone hard enough to send them into long term unconsciousness should leave them severely injured, if not kill them outright left unattended, yet doing so does not net you negative karma. Well of course it doesn't, positive karma doesn't mean being a total pushover only following Khan's philosophy of being inquisitive and merciful when possible rather then Hunters of eliminating every perceived threat with lethal force. Even if Artyom is still unintentionally killing many of the people he incapacitated like this he's trying to do as little harm as he can under the circumstances. It's the intent to be better that matters just as much as the necessities of the situation, even Khan killed some people after all.
The increased availability of pre-war weaponry like the Kalash can be chalked up to both the discovery of D6, and its massive stockpiles of weaponry as well as both the Nazis and Reds scrounging up their best equipment for the war everyone knows is coming.
Why is Anna easily captured by Lesnitsky without a fight during the raid on the Ranger outpost while also being able to wipe out a pack of Watchers and Nazi stalkers in the Chronicles pack? Because it was stated by Miller himself that she's the Rangers' best sniper, who are trained to fight from long range. With this, it's immediately apparent that she suffers from Crippling Overspecialization.
Why are the Nazis encountered in the main game all armed with only light weapons and armor, while the ones encountered in the DLC packs have much better weapons and armor? Because the levels where you encounter the former are set well within their territory, where such equipment and gear (i.e. armor and gas masks) aren't necessary.
Even in the good ending, it is revealed D6 is not a treasure trove of food and medicine that the Metro believes, but rather is full of weapons such as tanks, nuclear ICBMs, small arms and various biological weapons. How long before any of those are stolen again, especially the bioweapons? Downplayed slightly by the fact that gasoline is very hard to come by, and most nuclear weapons need regular maintenance, both of the warhead itself and all of the associated parts and propellants. With the way the games avert Ragnarök Proofing, most of the weapons they found are of questionable usefulness.
Lesnitsky was an infiltrator in the Rangers, working for the Reds. How many others are there? Who's to say that Artyom gave up all the information Korbut needed to stage the assault on D6?
Fedor was urging the slacking off guard to lock the gates before something nasty slips into the station just a few minutes before one of the fishermen gets dragged underwater and never comes back.