Carseats often don't fit through the scanner, especially if a carryon sizing template is fitted on the machine. If the stroller or the carseat is really too large to fit through, then you can have it scanned by hand. Expect TSA to insist that you TRY to put them through, however. Just cooperate rather than arguing about it, as seeing is believing, and they won't risk cramming it and possibly damaging the scanner.
When a manual scan is done, you must prep for it just as though the stroller was folded and placed on the belt -- nothing may be left in the basket or hanging from the bar. No toys left sitting in the seat, either. All such items must be removed and put in a bin for scanning. The agent will indicate where to bring the stroller or carseat to turn it over to them (usually whereever the disabled passenger line is), you roll it over, then you go through just as you normally would, and reclaim it from the other side when they have finished inspecting it.