Some of the biggest brands in the U.S. had ads running on the YouTube channels for far-right website InfoWars and its founder, notorious conspiracy theorist Alex Jones, and they say they had no idea YouTube was allowing their advertising to appear there.

Last week, YouTube reprimanded the conspiracy theory site and Jones for violating its community guidelines after a video posted to The Alex Jones Channel, InfoWars' biggest YouTube account, claimed student anti-gun activists were actors.

Now YouTube and Jones' channel on it are in the spotlight again. CNN has discovered ads on InfoWars' channels from companies and organizations such as Nike (NKE), Acer, 20th Century Fox, Paramount Network, the Mormon Church, Moen, Expedia (EXPE), Alibaba (BABA), HomeAway, Mozilla, the NRA, Honey, Wix and ClassPass.

Even an ad for USA for UNHCR, a group that supports the UN refugee agency UNHCR, asking for donations for Rohingya refugees was shown on an InfoWars YouTube channel.

Many of the brands -- including Nike, Moen, Expedia, Acer, ClassPass, Honey, Alibaba and OneFamily -- have suspended ads on InfoWars' channels after being contacted by CNN for comment. The companies, with the exception of Alibaba, which declined to comment, said they had been unaware their ads were running on The Alex Jones Channel. CNN discovered the HomeAway advertising shortly before publishing this story, and has not yet received a response from that company.

InfoWars and Jones are known for peddling conspiracy theories, including the false idea that the Sandy Hook Elementary School shooting in Newtown, Connecticut, in 2012 was a hoax.

Related: InfoWars' main YouTube channel is two strikes away from being banned

The brands purchased ad campaigns from YouTube, which is owned by Google, or through marketing companies that broadly targeted demographics and user behavior. Companies that purchase ads this way don't necessarily know where their commercials will eventually show up, but they can use exclusion filters to avoid having them appear on certain channels and kinds of content.

Several brands expressed concern about the ads' placement to CNN and said they have reached out to YouTube about the situation.

A Nike spokesperson said the company was "disturbed to learn that we appeared on [The Alex Jones Channel]." It has since asked YouTube to address why the channel wasn't flagged by a filter it had enabled.

Nike, like some of the other brands, opted in to a "sensitive subject exclusion" filter to better control where its ads appear. The exclusion filters include, according to YouTube: "Tragedy and Conflict;" "Sensitive Social Issues;" "Sexually Suggestive Content;" "Sensational & Shocking;" and "Profanity & Rough Language."

YouTube did not respond to questions from CNN about whether the channels should have been excluded by any of those filters.

"We have a filter and brand safety assurances from Google our content would never run around offensive content," a Paramount Network spokesperson said, adding that the company is trying to find out what "went wrong."

An Acer spokesperson confirmed the company also had reached out to its partners at YouTube, saying its "existing filters should have prevented this." The spokesperson said the company has set up additional filters to further block its ads from appearing on "divisive channels in the future."

"We take great measures to ensure our ads do not run on videos with sensitive content," a spokesperson for Grammarly, an online grammar-checker tool, told CNN on Friday. It was aware their ads had run on an InfoWars channel, the spokesperson said, and had been working closely with YouTube to ensure it didn't happen again.

A half hour after it sent CNN that statement, Grammarly ads were still running on an InfoWars YouTube channel. Its ads were also running on a YouTube channel that did not appear to be explicitly affiliated with InfoWars, but reposted InfoWars videos.

A Grammarly spokesperson said on Saturday the company had not been aware of the ads. "We have stringent sensitive subject exclusion filters in place with YouTube that we believed would exclude such channels. We've asked YouTube to ensure this does not happen again."

CNN has asked YouTube for further comment, but has not yet heard back.

Honey, a company that finds discounts for shoppers online, told CNN it unknowingly spent $169.64 to promote its brand on the Alex Jones YouTube channel. Honey said its first video ad appeared on the channel on January 21 and that eventually its ads on the channel received about 300 plays per day.

"[It] clearly was outside of our expectations [that this would happen by] using their sensitive subject exclusions tool," Honey co-founder Ryan Hudson told CNN.

The company's ad continued to play on The Alex Jones Channel until Wednesday, when CNN asked if it had any comment on why the ad was running there.

A spokesperson for 20th Century Fox said the company was unaware its ad had been placed on an InfoWars YouTube channel and after learning it had, immediately took it down. The company believes that it existing filters should have prevented it showing on the InfoWars channel.

The company is now having further conversations with YouTube, the spokesperson said, "to make sure this never happens again," and has asked for a refund.

A spokesperson for Mozilla told CNN, "We have explicit exclusions set up for our YouTube campaigns and should absolutely not have appeared alongside this content. We are disappointed to learn that YouTube's filters are not as effective as promised in preventing advertisements running alongside objectionable content. We've since reached out to Google and paused our advertising on the channel."

A spokesperson for USA for UNHCR said that this was the group's first time running ads on YouTube, and that it would now pull its ads from all of YouTube, and has asked for money spent on InfoWars-related channels back.

And a spokesperson for the Church of Jesus Christ of Latter-day Saints told CNN it has paused the specific ad campaign that ran on an InfoWars YouTube channel, and are looking into whether other ad campaigns are similarly affected.

Related: USA Today publishes op-ed by InfoWars conspiracy theorist

Companies can prevent their ads from appearing on any channel, at any time, by adding those channels to their account's "blacklist." Some of the companies CNN spoke with said that when they purchased ads on YouTube, they specifically included some of InfoWars' YouTube channels on their "blacklist," but that they were unaware InfoWars had other YouTube channels.

These moves come nearly a year after YouTube suffered an advertiser backlash when brands learned their promotional posts were appearing alongside extremist content.

Late last year, YouTube CEO Susan Wojcicki said the service would take steps to ensure advertisers "that their ads are running alongside content that reflects their brand's values."

YouTube declined to comment on InfoWars and content similar to it not being flagged by the "sensitive subject exclusion" filter but emphasized its commitment to being "an open platform."

"We uphold free expression according to our Community Guidelines, even when there are views we don't agree with," a YouTube spokesperson said. "When videos are flagged to us that violate our guidelines, we immediately remove them. We do not allow ads to run on videos that deal with sensitive and tragic events."

Honey is currently "investigating options with Google" to recover the money it spent.

It's unclear if Jones has specifically profited from the ads. YouTube allows channels with over 1,000 subscribers and 4,000 annual watch hours to be monetized. At least seven out of the 11 InfoWars-related YouTube channels fall into this category, including the Alex Jones channel.

A source with access to YouTube's Creator Studio management system said the videos on the Alex Jones channel are claimed by Jones' media organization Free Speech Systems, LLC. Depending on which policy an advertiser selects, a share of the money it pays YouTube could go to Jones' company.

Infowars did not respond to a CNN request for comment.

In the meantime, UK-based financial company OneFamily said it "alerted Google to recommend they add [The Alex Jones Channel] to their own blacklist."

--CNN's Donie O'Sullivan, Soukaina Alaoui El Hassani and Seth Fiegerman contributed to this report.

Update: This article originally said one of the ads running on the Alex Jones Channel was for UNHCR. In fact, it was for USA for UNHCR, a non-profit group that supports UNHCR.