Some advertising-technology companies have cut ties with Newsweek Media Group over concerns about allegedly fake website traffic, moves that threaten to exacerbate the company’s financial difficulties as it contends with a wider fraud investigation.

AppNexus, one of the vendors NMG used to sell online ads, and SpotX, an ad-tech company that helps sell video ads, each said they have ended their relationships with the company. They cited concerns over invalid traffic on the publisher’s International Business Times websites.

Meanwhile, DoubleVerify, a company that offers software for advertisers and ad vendors to authenticate the quality of the locations where their ads appear, has flagged four

IBTimes sites and Newsweek.co.uk as having invalid traffic. The warnings signal marketers that the sites are risky to buy ads on.

NMG said Wednesday it had fired two employees connected with the ad issue, but the developments nevertheless have the potential to scare off advertisers and add to the turmoil surrounding the parent company of the storied Newsweek magazine brand. The company already faces a wide-ranging investigation led by the Manhattan district attorney’s office into suspected bank fraud, ties with a bible college in California and alleged advertising abuses, The Wall Street Journal has reported, citing people familiar with the matter.

NMG has declined to discuss details of the district attorney’s probe or the company’s financial situation.

How much of an impact the invalid-traffic allegations will have on NMG’s advertising revenue isn’t clear. Like most publishers, the company works with a range of vendors to sell ad inventory across its sites using automated software. It retains relationships with several other ad-tech partners.

Beginning almost a year ago, DoubleVerify’s fraud lab started spotting patterns of invalid traffic on IBTimes.co.uk, said DoubleVerify Chief Executive Wayne Gattinella, and Matt McLaughlin, its chief operating officer.

Code running on the sites made it appear to measurement companies that browser tabs in the background that had Newsweek or IBTimes content were visible to website visitors when they actually weren’t, according to DoubleVerify.

The technique could be used to artificially inflate the performance of a website’s ads, leading advertisers to pay more, according to DoubleVerify.

NMG issued a statement Tuesday saying it had removed the codes from its website. Mr. McLaughlin said that as of Wednesday morning, DoubleVerify was still observing a similar code across some NMG sites, although it wasn’t clear how often it was being activated.

“DoubleVerify has never observed a legitimate reason for a publisher to implement” such a code, Mr. McLaughlin said.

On Wednesday, an NMG spokesman said: “Two of the engineers who were linked to this code issue have been let go,” adding that the company was conducting a thorough review of all of its sites to ensure they were free of potentially malicious code.

The spokesman added that its latest report from the ad-verification company Moat, conducted between Feb. 28 and March 6, found the latest invalid traffic rate across its websites, at 1.52%, was below the 3.1% industry average. The company soon plans to regularly publish its invalid-traffic numbers on its corporate site that have been verified by partners accredited by the Media Rating Council.

The spokesman said the company has “full confidence in the quality of our traffic and takes it very seriously.”

DoubleVerify has given IBTimes.com, IBTimes.co.uk, IBTimes.co.in, IBTimes.sg and Newsweek.co.uk its “Sophisticated Invalid Traffic Sites” designation. The label is a red flag for ad-tech vendors, who can choose whether to block those sites. DoubleVerify automatically prevents its advertiser customers from appearing on such sites

DoubleVerify says the classification isn’t an assessment of whether the site was aware of or participated in invalid-traffic practices.

SpotX, a video-ad-selling platform owned by RTL Group, and Teads, a video ad tech company owned by Altice, both stopped selling IBTimes traffic because of DoubleVerify’s identification of abnormal traffic, the companies said.

DoubleVerify’s findings add to allegations that NMG defrauded advertisers.

A February report from ad-monitoring consultancy Social Puncher alleged NMG had inflated its audience numbers by purchasing low-quality web traffic. In its response last month, the publisher said it didn’t engage in any kind of “traffic gaming techniques.”

AppNexus says an internal team had spotted a pattern of suspect traffic on and suspended the account “several weeks” before BuzzFeed reported on the Social Puncher study. After it was published, AppNexus says it terminated the account altogether and blacklisted other IBTimes properties.

On Tuesday, NMG announced it was splitting its IBTimes and Newsweek brands into separate operating entities, although the full scope of the restructuring wasn’t clear. Over the past year, the company has shifted resources from IBTimes to the Newsweek brand, and changed its name to Newsweek Media Group from IBT Media.

The company also began laying off some editorial staff this week at its IBTimes operation in India, two people familiar with the matter said. NMG’s spokesman declined to comment when asked whether layoffs had taken place.

Write to Lara O’Reilly at lara.o'reilly@wsj.com and Lukas I. Alpert at lukas.alpert@wsj.com