About the first or second time I started to sample some of my homebrew I noticed it poured kind of chunky. Upon closer inspection there was roping white shit in the the bottles, a kind of mold.
Of course, we were using bottles we had purchased full of beer, and had just drank them and tossed them in the pile to reuse. They had grown mold on the bottom and then we put fresh beer back on top of it. The mold appreciated the food but about half of the bottles were infected and gross.
So the homebrewer is faced with a dilemma. Empty bottle are kind of expensive so the logical option is to buy them full of beer. However, cleaning them is a chore.
This is what I do. When I empty a bottle I, IMMEDIATELY, rinse it out. It is pretty easy, I pour the beer into a glass and then flush the bottle with hot water and let it drain. This way they go into the box clean. If a bottle has sat long enough to get some shit growing in it I throw it away.
When it is time to bottle I wash all my bottles and run them through a soak with Star San. Occasionally I will get an infected bottle but it is pretty rare.
Like anything else with homebrewing, don't be a cheap ass. It is pretty easy to source bottles from a bar, or a friend who drinks a lot of beer, but most of the time you will spend more time cleaning the gunk out of the bottom of them than they are worth.