I'm Surprised I've brought up this earlier but the Normandy lockdown scene that occurs in ME1 after completing all four plot makes no sense at all and is in my opinion the weakest part of he game. My primary gripe with it is that it relies on many (incorrect) assumptions that logical person simple could make. Let's just go over them right now:
1. The Turian councillor says Shepard belives that Saren will attack the Citadel. However Shepard only learns of Saren's intetion to mount an attack on the Citadel when conversing with Vigil on Ilos, which obviously only happens after the Normandy has left the Citadel. Prior to that Shepard knows little of Saren's exact course of action, other than finding the Conduit which is hidden on Ilos.
2. Udina says Saren's greatest weapon was secrecy, and that exposed he is no longer a threat. Arguably the most blatent plothole in the scene, If this was truly then why did Udina put so much effort into making the Shepard a Spectre. Saren was already exposed after Tali's evidence was presented yet it was Udina insisted into making Shepard a Spectre so that he could deal with Saren, once again this is the most nonsensical stament of the scen and can only be taking seriously if Udina was blatently lying at this point.
3. Udina says Shepard's becoming more trouble then s/he's worth. Udina doesn't provide us with any evidence to back up his claims, He appearantly just says this to get rid of Shepard. Yet Shepard was doing fine up until this point and I don't see any particular motive as to Udina wants to get rid of Shepard as a Spectre, Shepard has been helping humanity and the Alliance (remember all those messages from Hackett) from the he was made Spectre and there is no reason why Udina would want Shepard out of the way.
4. Udina orders the lock down of the Normandy. This aspect makes no sense for two reason: 1. A civil ambassador has no authority to instruct a foreign police force (C-Sec) to lock down a military naval vessel. Either the Council should ordered the Lockdown themselves or the Alliance military Should have disabled their own vessel. 2. Shepard's a Spectre and therefore can ignore the instruction of any civil or military authority other than the Council itself.
The only way this sense makes any sense is if Udina and the Council had been conspiring from the beginning to lock Shepard down after dealing enough damage to Saren and the Geth and were blatently lying to Shepard when they made these statements.
This scene could have been easily fixed by just having the council thanking Shepard for his efforts against Saren but stating that his part in this fight is over and that the Military is taking over now. Admiral Mikhailovich shows up and the Normandy is formaly turned over the Alliance and will depart for Arcutrus with a few hours. The rest of the game can then proceed mostly as is.