Last week, the world's biggest social network was criticised for switching the default email addresses on profile pages to @facebook.com addresses without first asking its 900m users.
However, this has been followed up by some smartphone users, particularly those on older Google Android devices, reporting that their on-phone address book has also been automatically updated to @facebook.com accounts.
This means that any emails sent by affected users to their contacts automatically go to the @facebook.com address as it is the default contact address.
Mark Zuckerberg's firm blamed the deletion of users' contacts on a software glitch, which will be "resolved soon".
Facebook declined to comment on the scale of the bug, or which users were affected.
Many users have criticised the glitch, particularly as they may have sent emails to their contacts into addresses that they don't actually use.
One affected user told Hacker News earlier in the week: "This morning my mother was complaining that many of the email addresses in her Droid Razr contacts had been replaced with Facebook ones.
"It would seem the Facebook app had been populating her address book with emails and contact photos, and decided to migrate all her Facebook-using contacts over to this convenient new system. That seems like a much greater controversy to me than Facebook hiding people's email addresses."
Facebook said that the issue was connected to the application programming interface (API) in a tool designed to keep its users' smartphone contacts up to date.
The software was written to copy over all "primary email addresses", and as this has been @facebook.com accounts ever since the change of approach last week, third-party addresses were therefore being bumped from the default.
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Facebook's statement acknowledged that "for people on certain devices, a bug meant that the device was pulling the last email address added to the account rather than the primary address, resulting in @facebook.com addresses being pulled".
Security blogger Graham Cluley said that Facebook's change of users' email addresses to @facebook.com accounts had been "one monumental screw-up".
"I believe the site was trying to get more people to adopt @facebook.com email addresses for their regular communications, to make their dependence on Facebook even greater," he wrote in a blog post.
"But they've ended up with more disgruntled users, who will be wary of the next time Facebook changes things without proper notification and without thinking of the repercussions."
Anyone wishing to undo the email change on their Facebook profile can access the About section on their profile page and then click Edit next to the contact information.
This then opens up an option to 'hide' the Facebook email address from your Timeline, and replace it with another email address if you so wish.