In season four, Michael looks at a picture from when he was a kid, where he, Lincoln and their parents are present. But in season two, it's revealed that Michael has never met their father, and their first meeting is set in season two.
When Sara hits the car driven by Michael's chasers, you can clearly see the men inside are dummies.
As the "Company" operatives try to sedate Michael you can see in the mirror, for a split second, a boom mic. At around 35 minutes.