You can definitely blame the deconstruction aspect with TVTropes since they love to throw that word around. A correct way of deconstruction would be that in the first few hours/episodes, the application of the genre you want to deconstruct, is shown but around the near middle, the gloves slowly comes off until the the finale where the protag is no longer using the tools of the genre, in this case, magical girls and robots.
Let's say you want a deconstruction, let us use an example: war from the perspective of a soldier. First things first, you gather the most popular parts of the genre, the usual platoon that you side with, military propaganda, gun porn, "fight for your country" crap. You establish those on the first few hours. You're a regular grunt in some shithole country that you were conscripted for and now you have gone through rigorous training to be a part of the corps. You get introduced to your squadmates, the guns you hold and your orders as you are about to be deployed in the warzone. Fine and dandy, you get yourselves something out of Call of Duty on the first scenes. This is your established genre that you will deconstruct later.
Near the climax, after hours of receiving orders and clearing some militias, the protag you get introduced to starts to slowly question his role (don't make this too abrupt or obvious, show small details like him staring at a window of an abandoned house or maybe something like putting his hands in his pocket when the soldiers are ordered to scavenge from the dead corpses). When the squad camps out for the night, let your character contemplate, maybe stare at the night sky as the squad talks. Then some event happens to the platoon, maybe they got ambushed in the night, or after moving to the next area, they get separated. During this time, your character, without interference from the soldiers and radio, gets to look at the whole battlefield they have been deployed to, show dead civilians or whatever. You can let your MC drop their gun out of disgust or march forward until another platoon shows up but does the same thing, seeing that you and your lost platoon have been dispensable and that the nonsense killing. Instead of a potential rendezvous, the MC backs off, maybe have him fight a scurry of rebels or even another platoon. This part is where the genre shifts, instead of following the usual traits of the genre, you show another perspective, how fucked fighting is and how they are just cogs in the machine.
Lastly, as the climax fades, your MC finally recovers but they are in the middle of nowhere, no supplies, no soldiers nor gunshots, nothing. Seeing that the battlefield is no more, the MC decides he's done with the military service and instead plans on going home. He throws the guns away, takes off the uniform, tosses his weapons out and leaves. During this part, you can do whatever you want: maybe in the end he does get home but has to go through the wilderness, maybe he ditches the aspect of going to civilization and live for himself, maybe he can try posing as a villager and live a different life. This part is where the gloves are no more, no more guns, military or lingo mumbo-jumbo. It deconstructs war and the genre surrounding it. No subversion, no going back to those tools, nothing. You ditch those and try to choose a better life beyond just shooty.
This is just the concept. Then you can either use animation or live-action to scene it out, use cinematography, camera angles, all the tiny details to make it look real. Maybe you can add additional scenes that can help enhance the original draft so long as the middle and end are still faithful to the idea of a deconstruction. If you say that "the guy gets his gun back", that's not deconstruction, you created a subversion and you failed in the former if that was the intention.
