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A Facebook spokesperson confirmed to Variety that this also impacted internal apps used by the company's workforce, and multiple reports indicated Wednesday morning that the company was caught off-guard.

A Facebook spokesperson disputed portions of TechCrunch's report in a statement to Fox News, claiming that key facts are being ignored.

The Facebook Research program came to light yesterday, but it was something of an open secret. It said that less than 5% of those who participated in the research were teens who signed parental consent forms.

The kind of data Facebook could access includes private messages and chats from apps, internet searches, emails, web browsing activity, and location information, as noted by Guardian Mobile Firewall's Will Strafach. Due to this move, thousands of Facebook's employees are now unable to access their internal iOS apps. Following the revocation, those employees had to download released versions of the iOS apps from Apple's App Store.

Facebook said Project Atlas doesn't violate Apple's Enterprise Certificate policy, but the certificate program is primarily created to allow employers root access to employees phones.

"We designed our Enterprise Developer Program exclusively for the internal distribution of apps within an organization", an Apple spokesperson said.

But Apple's response also hit some of the basic infrastructure built into Facebook's offices, particularly its headquarters in Menlo Park, California.

"Like many companies, we invite people to participate in research that helps us identify things we can be doing better", Facebook said.

On Tuesday, the company defended the research app, saying that it was up front with participants about how their data would be collected. Google probably has a higher distribution of Android devices than most companies, but having a good chunk of your employees' smartphones go down, in addition to having iOS app testing halted, sounds pretty bad for productivity.

Earlier this week, Apple banned Facebook from running internal iOS apps because Facebook had been using Apple's enterprise certificate to distribute software outside of the App Store.

Still, the blowback for both companies raises questions about how much consumers really understand about the information they are giving up, and whether the companies' approach to seeking permission is sufficient.

Facebook has not yet responded to The Daily Caller News Foundation's request for comment about Apple's decision. TechCrunch's investigation found that starting in 2016, Facebook had been working with three app beta testing services to distribute Facebook Research: BetaBound, uTest and Applause. It's permission-based, and Facebook has apparently being paying the users who participate, but this has nevertheless generated yet another serious black eye for Facebook, which bypassed Apple's App Store and seemingly broke some of Apple's rules to do this.

Facebook CEO Mark Zuckerberg recently penned a 1,000 op-ed in the Wall Street Journal jumping to the defense of his company's business practices.

Facebook distributed the app to consumers through Apple's "Enterprise Developer Program".