The tech giant activated the tool following the explosion which asks users in the area of a disaster to share if they are safe.
It said a system "bug" was to blame for the mishap.
"Unfortunately, many people not affected by the crisis received a notification asking if they were okay," the company told CBC News in a statement.
"We worked to resolve the issue and we apologize to anyone who mistakenly received the notification."
Many people were left confused when they received the notifications and even text messages asking them whether they were "affected by the explosion."
It led some as far away as B.C. wondering if something dire had happened closer to home.
Facebook would not comment on how many of the messages were sent out but that it was "counter to the product's intent" and the problem had been resolved.
The company has previously been criticized for selectively activating the tool — choosing to use it following the attacks in Paris but not in Beirut.