Chris the reason you saw them shovel a pile of bottles or a bail into the landfill is that the bail most likely got contaminated.
In recycling, like anything the Recycling facilities do their best to try make their bails as pure as possible, i.e. a bail of HDPE, or LDPE, or a bail of Steel, or aluminum...typically these bails are kept above 96% purity. However if a bail comes off of the line and is a mess there are a few options, you can try find a processor to buy the bail at a heavy discount, you can throw the bail back through the system, or you can simply toss it in the trash. If the bail was heavily contaminated with something really bad, i.e. lets say a few gallons of used motor oil made its way into the bail then you basically are forced to throw it in the trash.
Dependant on the MRF there are different efficiencies for sorting as well. Some private Recycling facilities such as the one that does a large part of peterborough actually throws out 15% of the reyclables no matter what simply because their sorters are crap, so whatever doesnt get picked off of the line literally gets tossed in the trash once its made its way through the facility. State of the art ones like the one Durham just opened say they reach up to 98% efficiency...which all things considered...in the early 80's kitchener was the only place recycling and the rest of the world was throwing basically everything but cans and steel into the trash.
We are doing pretty good, and it will only get better with time. Certain countries in europe are literally going to 0 waste...i.e. even stuff thats hazardous will be collected and managed appropriately. So complain all you want about a small bag costing money, soon you wont even get that, its just a matter of time.