I'm gonna take another crack at this.
Anderson looking at shepard directly to the eyes while supposedly talking to TIM about reaper influencing him
So they fucked up scripting some dialog. Wouldn't be the first time. The game probably has characters in dialog look at Shepard by default since that's going to be the case 90% of the time and they just forgot to override it.
stupid oily shadows on your dreams
An aesthetic choice, but not necessarily a meaningful one. Someone probably just thought it would look cool. Seriously, I'm having trouble figuring out how this could be a sign of indoctrination when it isn't mentioned in the codex entry, or anywhere else that I can remember for that matter.
You've brought this up a few times and I still have no idea what you're talking about.
the catalyst being able to read your mind and take the form of a ghost child that was never anywhere but in shepards imagination to begin with
Bad writing. I doubt Bioware even knew what the fuck the ghost kid was supposed to be. Remember, the head writer basically wrote the entire ending sequence alone and it wasn't peer-reviewed, and apparently none of the other writers were happy with it.
anderson dying and you having a wound in the exact same spot
The scene is supposed to show Shepard dying, and they only have one hurt animation. So it's either make an entirely new animation that will only be used once, or use the generic gut-punch one they've been using since ME1. I'd have to look but the wound is probably in the exact same place because they copied the texture and bleed effect too.
the shadows of anderson and TIM completely opposed
Could be intentional, but nothing about this screams "indoctrinated" to me. More likely it was just supposed to emphasize the conflict between synthetics and organics, or something like that. Or it could be a lighting bug - maybe they had to do something weird to get shadows to work because of the lighting in that room, or something.
and even if they swich positions their shadows remain in a static angle
They probably set the shadows up to be static so they could get the effect and forgot to move the shadows when the characters move, or the scene was changed and someone forgot/was too lazy to edit the shadows later on. A minor aesthetic detail like this would be missed by 99% of players (I know I did, but I was furious by this point in my ME3 playthrough, so...) and it would be very low priority to fix if it was caught by QA.
harbringer never targeting shepard directly with his laser, when he was insta disintegrating everything that came close to that beam of light.
Bad writing, and a common action cliche. The reapers at the beginning of the game do the same thing when they blow up the transport with the star kid on it instead of the armed warship launching from the surface 50 feet away.