If I went through the visual novel again I feel I could nit pick a ton about the animation vs VN.
Here is a big one. The Junker does not lose his backpack in the VN because it has the spare rain coat that Yumemi later wears in it! Also it looks like he had lots of packs of rations/heatpacks/bandages in his bag which goes against the VN when he counts out what he has in his bag.
One you can see on the Steam store page is the scene with his grenade launcher which is green in the VN compared to the traditional M79 he has in the animation.
The Junker wears urban camouflage in the VN by his description, which is insulated against the thermal visions of the drones but as we see in the animation, they can see Junker without it.
In the visual novel, Junker covers his face with streaks of mud to further combat the thermal vision of the drones which he does not do in the animation. (Unnecessary because they have changed the intro into a combat scene)
In the battle with the fiddler crab in the VN, the fiddler crab does not use it’s main cannon (rail gun?) against the Junker when he is in the building like it does in the PV, it fires its machine guns.
Some quick details/notes from the visual novel can be found on the glossary on this page