Well I've seen a lot of posts on the where the Reaper's logic doesn't make sense, but here are some more:
1. Their attack. In Mass Effect 1 we learn the Reapers enter the galaxy through the Citadel relay, kill the governments of the galaxy and then take control of all the Mass Relays through the Citadel. In Mass Effect 3 they for some reason start attacking the home-worlds 1st, then they move on to the Citadel. They are then able to move the Citadel to Earth (how and why?), but don't use it to take control of the Mass Relays. This makes no sense.
2. Citadel. In Mass Effect 1 we learn that the Citadel is a giant Relay connected to dark space. It is then activated by the Reaper Vanguard when it deems it the right time for the cycle to commence. It is also revealed the Citadel was made by the Reapers. In Mass Effect 3 the Citadel is revealed to be the master of the Reapers - this makes no sense at all.
3. Reaper effectiveness in combat. In Mass Effect 1 a single Reaper manages to destroy most of the galaxy's combined fleets. In Mass Effect 3 a Reaper fleet is not even able to successfully destroy a fleet even though they have superior numbers.
4. The Reapers never find the Crucible. This makes no sense.
5. The Reapers never used indoctrination on the people it would have made sense to indoctrinate (e.g. Turian Primarch, Admiral Hackett, Anderson, Shepard, etc).
6. The Reapers are not able to win in Mass Effect 3. I am particularly appalled by that there is not an ending where the Crucible gets destroyed by the Reapers if you have a low readiness.
What I find interesting on most of these contradictions are that they contradict Mass Effect 1. More specifically that they contradict things that only someone would know who either played ME1 or someone who read up on ME1...
Anyone else feel that the real blame for the atrocity of a finale can only be placed on Bioware for dumbing down the story for people who didn't even care enough to play or read about the previous games?