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Ok, so, I am currently writing a book and 3 of my characters have the same name as in another novel. I didn't realize it until someone pointed it out to me. The names I picked are fairly common and used frequently in the real world. Is it a problem? Even though the books have absolutely nothing to do with each other? Do I have to change it for safety?

PS: The names are: Emma, Oliver and Jacob. Same names as in Miss Peregrine's Home for Peculiar Children

The answer to your question depends on how strongly the set of names is associated with the preexisting work of fiction. Not just the individual names, but the set of names together.

For example, individually Romeo and Juliet are common enough names, if you set your story in Italy. However, if you name the main characters in your story Juliet and Romeo, it would be read as a direct reference to Shakespeare's work. On the other hand, if I were to write a story about Robert and Maria, I very much doubt you'd think of For Whom the Bell Tolls. In fact, I would be very much surprised if there aren't countless other stories with the same names.

You are free to reference another literary work, that's called intertextuality. However, such references should be deliberate, not accidental. Names are one way, not the only one, and not a necessary one, for creating intertextual links.

As far as copyright goes, one cannot copyright common names. Or even sets of names. I'm not sure one can copyright names one has made up. (A character would be protected by copyright, but that would include additional attributes.) Consider, we are seeing quite a few girls named Khaleesi. In a few years, one might write a biography, or a fictional biography, or just a work of fiction, about a girl named Khaleesi, similar to how a character in Good Omens has been named by her hippie parents Pippin Galadriel Moonchild (a reference to The Lord of the Rings and The Neverending Story).

So, if you're asking about the legal aspect of things, there's no problem there, and that would be true regardless of what particular names you have chosen for your characters. If you're asking about other aspects of the issue, you should ask yourself how strongly the names are associated with the preexisting work. In your particular case, I do not believe there is a strong association. In other cases, the answer might be different.