Things that don't make sense (v2)

That's right, it wasn't explained. Nevertheless I disagree with your statements:
- Shepard was walking forward to the train station cleaning up the scene, which he stated in the playthrough when talking to the farmers hidden in the shed; hence it's just theoretical, but actually impossible to be true to mess the Nihlus' body by geth on the docking platform.
- yes, the Council does act stupidly, because the motives behind their actions are either doubtful or unknown; they shut down the investigation, that's true. They never wanted spectres investigated - also true, but it still doesn't make any sense considering the facts, they had sent Spectre for a crucial mission and somehow another Spectre, after a fiasco, becomes indicted of a murder. Also how would they not get any intel, even the smallest part of what might have happened on Eden Prime as it was?
- At least in my view, and that's how all things should work, there must/should be some other agents who know how things work and would be able to investigate the crime scene, meaning spectres, to avoid involvment of the outsiders (C-Sec); just like any other agencies do - FBI; CIA; etc.);
- It would make more sense, if Saren was banging the Asari councilor, was the best friend with Turian councilor or sth like that, and knew some dirty secrets of Salarian councilor, implying Saren could blackmail, hold them for their balls/boobs. Hence the only way to make the Council revoke him of Spectre status, would be exposing him publicly as in the game. Also, why would they let one of their fellas act like this, not paying any consequences, while they had been preparing this crucial mission that might further speed up their technology for a few hundred years forward? Mind You, in ME3, on Thessia, Asari government kept Prothean tech. secret the whole time, so it must have been very important for everyone to get the beacon untouched and secured. I couldn't imagine they would just let a spectre go with that mess.

Because we have some serious accusations and some evidence support, as mentioned before in previous post, I'm ready to admit that the Council part has some flaws. Not as ridiculous as in the recent "!%@&(^:A" game, but still worth mentioning.

"One thing I didn't quite understand though:
"but it still doesn't make any sense considering the facts, they had sent Spectre for a crucial mission and somehow another Spectre, after a fiasco, becomes indicted of a murder. "

Who is who in this?"

- You got it right - the Council sent Nihlus, then Saren was indicted of murder. Let's just assume, as it's been stated here and in the game, that Cpt. Anderson and the Allience dudes are just pest, another race with bad reputation, like krogans - untrustworthy. It doesn't release the Council from its responsibility to get to know of what had happened. There we may go with the argument that another spectre agent should get into it. We agree on it and that's cool.

- About the ballistics, I mentioned an interesting thing in my first post about the Samesh Bhatia quest. What's more, from what I've checked on the mass effect wiki, various weapons have different acceleration when fired given to a metal slug or sth, and they seem to shoot out differently, which is mentioned in the codex and wiki site.

"Weapons in the Mass Effect universe are micro-scaled mass accelerators, using mass-reducing fields and magnetic force to propel miniature slugs to lethal speeds. Nearly every gun on the battlefield is laden with features, from targeting auto-assists to projectile shavers that can generate thousands of rounds of ammunition from a small, internal block of metal."

It's also easily noticeable during the gameplay, so You don't have to be a specialist to know that shotguns from a close range would blow Nihlus' head away.

We didn't really hack the Omega-4 relay so much as put an IFF on our ship that identified us as "friend" and so survive the trip.

I'm also not sure anyone knows enough about relays and how they work. Aethyta wanted to reproduce them but everyone laughed at her idea. I would guess not a lot has been done to study the relays.

Not sure why the asteroid destroyed the relay but not a supernova; however, can hazard a guess. The Mu Relay was far enough away that the shockwaves sent it hurtling through space before the explosion itself could wash over it. (My knowledge of this stuff is minimal so maybe I'm not making sense.) With the asteroid, it was just this physical thing hitting it with no warning so it destroyed the relay. Conjecture, of course, but maybe reasonable.

Why does Anderson tell Shepard twice, that he was born in London? Once in the comm room and again in the shuttle in London, with that shifty look on his face

Why are James' eyes not green if your crew survive in the Synthesis ending?

Apologies if these have been brought up before, but I noticed these during recent playthroughs....

If ems is below 2700, the catalyst will ask, "Why are you here?" when Shepard is on her/his hands and knees. Why would it ask that? Shepard had no control over the platform raising her/him up to the decision chamber.

If ems is above 2000, the soldiers are seen cheering in destroy and control endings, but they're not cheering during the synthesis ending. Why is that?

How does Joker manage to (audibly) crack his knuckles without breaking them enroute to the Geth Dreadnought?

the timing of Hackett calling to Shepard over the comms. Hold on. How does he know its Shepard? It shows him getting a datapad, but mentions that someone made it up, but doesn't know who. Lets turn the clock back. Didn't the voices on the comms say that no one made it to the beam? So who passed the message that someone made it to the beam?

Hackett calls Shepard saying the crucible isn't firing. It has to be something on Shepard's end. Shepard passes out. After that nothing. Why didn't he continue trying to get a hold of Shepard? Since he gets no response, why didn't he send a shuttle to Shepard's location? Maybe he did and it got destroyed. I doubt that since I'm sure a scene would've shown a shuttle headed towards the Citadel before it gets destroyed. Hackett has to know time is not on his side. Either way, I would've sent a shuttle to investigate. 

If Anderson did, then I would be curious why he didn't tell the others to not retreat but to head to the beam after Harbinger flew away.

Coates says, over the comms, negative when asked if anyone made it to the beam.

If Hacketts comms officer is tapped into Shepard's comms he would have heard the conversation between Shepard, Anderson and Coates after the reaper was destroyed. Anderson also said that Hackett told him some reapers are headed their way. There would have been no need for Anderson to ask one his guys to get a hold of Hackett after that conversation.

Ok. So why wouldn't Hackett send a shuttle to that location? Time is not on his side. What would he do if Shepard were to pass out a second time? Stand around twiddling his thumbs hoping for something to happen?

The other thing is since Shepard heard Hackett's voice, why didn't he/she make any effort to get a hold of Hackett after regaining consciousness? I don't care if the thing is talking or not. I would at least let Hackett know I'm still around.

That ending boy lol

It always comes up

What does Anderson have to do with that?

And once they know what's going on, they won't be cheering anytime soon. They'll most likely be trying to figure a way to get rid of the green crap on their bodies

Even if they did try, we saw the state of things.  Bodies littered the halls.  We don't know it's the way everywhere but it's not exactly unlikely.  Also, even if they reached someone, the Reapers probably controlled most of the doors and trams that would allow access, nevermind have the proper authority to do anything at all with the arms.