Things that don't make sense (v2)

Mass Effect 1's plot. I love the game, but Saren's actions are completely nonsensical.

As a Spectre Saren has full access to the presidium, as do the indoctrinated Asari commandos in his service. They could have easily seized Citadel control and no one would have ever seen him coming. With that in mind, Saren needing a backdoor onto the Presidium made zero sense.

He ends up outing himself as a traitor and losing his Spectre status while attacking a human colony for a Prothean beacon he didn't need, as the Conduit was completely useless to him before losing that Spectre status. To make matters worse, he already had a Prothean beacon on Virmire.

In retrospect I'm convinced that in an early draft of the script Saren probably wasn't a Spectre. Needing the Conduit only makes sense if Saren doesn't have full access to the Presidium. I wonder if in the original draft Saren had lost his Spectre status during his misadventure with Anderson.

I heard that at one point Benezia was supposed to be the main villain, but this was changed in the end due to casting issues, or something like that. This wasn't some official source or anything, so it may not be true.
Although, it makes sense if you think about certain things, such as 'Eden Prime was a major victory, the beacon has brought us one step closer to finding the conduit.'
'And one step closer to the return o the reapers.'
It makes sense if Benezia is in charge, because Saren saying about the short term goal, and then Benezia with the overall evil plan.

Also, Liara on Therum when she says she hates her mother and never spoke to her in years. This is especially weird when in the rest of the game she acts as if she and Benezia were close before.

There are lots of little things that may be part of an old draft with Benezia in game, but nothing solid, as Garrus would say.

I posted this a short time ago in another thread.

It doesn't make sense to leave either Ashley or Kaidan with the bomb. It makes more sense for a salarian since they're the ones who converted their drive core system into a twenty kiloton ordnance.

I had Kaidan with me on Binthu and it was Kaidan who told me that Cerberus had other bases on that planet... and we eventually discovered Kohoku's body in the third one. I had Kaidan with me when I we found Corporal Toombs about to kill Dr. Wayne for what Cerberus had done to him. Yet, at the very end of the game on Sigma 23 when Flores' journal entry indicates that they can supply a few groups of Cerberus commandos with rachni troops, Kaidan blurts out... "Cerberus, is that a corporation?" I mean, "Really... Kaidan?" Think I should run him into Dr. Chakwas to check for a serious brain injury?

... At least Wrex is impressed that "humans are consistently stupid."

I often play BDtS entering the facility with the mine field first; hence I meet Simon still inside that building. You miss out on being able to ask him whether you should requisition a cow, but you gain access to paragon/renegade selection—where you can comment on the mine field—that feels upside down to me.

Some minor oddities, since the big ones have probably all been covered:

1) In the ME2 Illium sidequest with the asari and the indentured quarian, Shepard has both a Paragon and Renegade speech that can be used to persuade the other businesswoman to hire the quarian, and IIRC, one of the two (I think the Renegade one) was just confusing. Not in the sense of "I don't understand why Shepard would say that" - more that I didn't follow the logic of it or how it would resolve the situation for the businesswoman or the quarian. (This could be more my problem than the game's.)

2) Who are the mercs shooting at you inside the base in the ME1 Toombs side mission? If they're Cerberus, then they must be the only Cerberus troops not marked as such by the game. If they work for Toombs, well...wouldn't Toombs have heard all the gunfire taking place out there before Shepard gets to him? And saying "I have no problem with you" to Shepard is kind of bizarre if they're his. ("Um, no problem except those dozen employees of mine who just tried to kill you, that is.")

3) In ME2, one of the sidequest chains for the mercs - I think maybe Blue Suns - takes an odd turn from "go around and shut down some merc operations" to "batarian extremists are trying to launch a missile at a colony" without, as far as I could tell, much explanation of how this tied together or even how any information recovered from the previous stages would have tipped off the Normandy crew about the missile launch.

4) Why is Miranda surprised that Shepard went back to the Alliance in her ME3 e-mail? She's already ditched Cerberus herself, and it's not like there was some other independent group out there looking to hire Shepard - the Alliance was the only other game in town for fighting the Reapers.

I've often wondered about the same thing with the mercs on Ontarom.  I now use the head canon that they are mercs Dr. Wayne hired personally to protect him after the other scientists died.  Toombs, working alone, managed to sneak past them to get to Dr. Wayne; whereas, Shepard being more of a bull in a china shop and not very stealthy, just shot his/her way into the facility.

You just made my day ... maybe the fish tank?... and they weren't dying because Shepard just forgot to feed them.

"Humans carry a lot of germs." (Tali, Citadel DLC)

Gramps Stargazer at the end of ME3 embellished the story he was telling his grandchild.

The truth is that the "Virmire casualty" didn't die on Virmire. Ashley/Kaidan took a shower in the captain's cabin and couldn't get the door open in time and drowned. The Kaidan Alenko Memorial Fund, if Kaidan died, wasn't really to send gifted biotics to Grisson Academy. It was to install working drains in all Alliance vessels.

After the destroy wave destroys the reapers, Alliance, Turian and asari ships are seen flying by the damaged relay. Why aren't quarian ships shown if they survived Rannoch?

It's Shepard's fault.  After getting punched out for pressing the attack on the geth dreadnought, Gerrel rethought his military strategy and decided that retreating from every battle as early as possible was the way to go.  So basically, the Quarian ships entered the system and then, as soon as the Alliance was thoroughly engaged with the Reapers and wouldn't notice, Gerrel ordered all the Quarian ships back out of the Sol system through the relay before it was damaged.  By the time Shepard "shoots the tube" (to use your expression for it), the entire Quarian fleet is already back at Rannoch.