The confusion meant many people effectively paid twice for the final 16 episodes of the hugely popular show.
This was because Apple charged people who bought a “season pass” twice – once for each eight-show chunk as they were billed as separate seasons.
Apple has sent out emails giving people an iTunes voucher for the extra cash they spent.
Breaking Bad Season 5 was split into two halves by cable channel AMC with each eight-episode section being shown a year apart. The second half of this season, which sees the show reach a conclusion, was first broadcast and made available online on August 11.
The split caused problems on iTunes where many people had paid to see the closing series expecting that this would include all 16 episodes.
When Apple charged people again for the second eight episodes, called The Final Season, many complained and one outraged fan took legal action over the extra charge.
Apple has refunded the extra $22.99 levied on those people who were charged extra to watch The Final Season. Those who bought a season pass for Season 5 will now be able to watch all 16 episodes.
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