Amazon employees have been mistakenly taking down ads with religious content, causing some small sellers to take a direct hit on their sales.

Multiple sellers have seen their product ads get suspended in recent months for having language about religion, CNBC has learned. These sellers were told by email that their ads were getting blocked due to a "new policy update" at Amazon which bans any ad that contains "religious content."

"Products related to a specific religion are not allowed to be advertised," an Amazon representative told one of the sellers in an email viewed by CNBC.

Now, Amazon says it was just a snafu. Amazon's spokesperson told CNBC in an email that there haven't been any policy updates and that its employees are being re-trained.

"The email that CNBC viewed contains inaccurate information and our long standing policies have not changed. Corrective training is being provided to the relevant teams," Amazon's spokesperson said.

The incident is the latest example of Amazon marketplace sellers getting caught in the crossfire as the company has struggled to manage the sprawling growth of the third-party marketplace, which now accounts for more than half of the company's e-commerce volume. For example, as Amazon cracked down on a growing problem with counterfeit products, bad actors have used fake counterfeit complaints to get legitimate sellers taken offline.

In this case, marketplace sellers were using Amazon ads to try and stand out from their competitors. Although Amazon makes the bulk of its money from e-commerce and selling computing infrastructure to businesses (Amazon Web Services), the company is also generating billions in ad revenue from companies who pay to have their products appear prominently in search results and other areas on the site.

The company's "Other" business segment, which consists mostly of advertising revenue, booked $2.72 billion in the first quarter, showing growth of 36% from the previous year (although that's slower growth than it saw in most of 2018), and Amazon is now the number-three digital ad player in the U.S. after Google and Facebook, according to eMarketer.