There's no evidence, only speculation. You guys are nuts.
Why did indoctrination all of a sudden resurge? I thought it was on its way out.
Ok...if there's no evidence, then why does Shepard have a gunshot wound in the exact spot he shot Anderson?
Why is the Illusive Man able to force Shepard to shoot Anderson with no control chip?
Why is the Reaper AI a child from Shepard's, and ONLY Shepard's, experiences?
The Rachni Queen references 'oily shadows' and voices of fear,
exactly what Shepard sees in his dreams of the boy.
Why is Shepard's body suddenly back on Earth at the end of the red option when he takes a breath, and not the Citadel?
All of these stand out as OBVIOUS signs to indoctrination, let alone the other inclusions of hints and suggestions, like the codex having an entire description of the indoctrination process, in complete detail.
There's also smaller hints, such as Anderson getting to the arm control panel first, Shepard's gun having infinite ammo, the same bushes/trees present in Shepard's dreams appearing around the Citadel portal after he wakes up, and on and on and on...
These aren't accidental plot holes, these are obvious, planted, signs pointing to a more detailed ending/resolution that actually makes sense.