If you're working the repair lines then you'll know if you tear apart a clone and compare to the genuine and you'll see there's notable differences. The protection/controller board attaching to the cell on those $4 batteries is a random hackjob at best. The cell quality too is different, cheap replacements have poor internal resistance compared to the genuine.
The $4~$12 replacements are a crap shoot, sometimes you get a decent quality unit, other times not so much. The resellers of replacement batteries give you grading options, cheap = 'zeroed' cycle count, non-original board, then you can get a "pulled from existing phone" batteries and their markings rubbed out, and then you can also get "Genuine zero cycles, high quality" packs but even if you ask for those, usually someone up the supply chain at some point pulls a swifty and starts sending you dodgy packs.
While Apple might pay $4 for theirs, the "3rd party" ones are probably $1 and it shows.
Apple has had some dud events like the iPhone 5 puffer fiasco but overall their packs definitely are of higher quality/consistency than the 3rd party replacements.
Couple of hundred batteries a year and it's averaging about 50% duds within 3 months.