Do not get confused by the to pipes being side-by-side in the first picture. There is not necessarily anything wrong with this, though in northern climates the moisture of the combustion gas will freeze at the intake and shut the equipment down.
The example they gave in how it should be done is the recommended installation practice but would not have been sufficient to protect the carbon monoxide issue because the air intake was not properly completed. The main issue was that the air intake was not piped all the way to the boiler. Combustion gases were being drawn into the utility room area not just into the furnace. Normally if piped properly, carbon monoxide would never enter the house because the intake/exhaust system is a closed loop.
This article is a bit confusing. If the pipe through the wall was intended as a fresh air makeup vent, then it must comply with gas appliance venting requirements. A mechanical draft condensing furnace vent termination must be a minimum of 3 feet above any forced air inlet (not furnace intake). A minimum of 1 foot above any building opening or 4 feet below or to the side of a window or door opening. The window in the photograph appears to be too close to the discharge.
Another problem was that the furnace was fueled by propane, but had not been converted from natural gas. I tried to post the article from the newspaper, but the link changed. You may be able to search and locate it.
In any event, someone died due to a chain of errors.
Here are a couple been more then this latly .