How to remove array element in mongodb?

Try the following query:

collection.update(
  { _id: id },
  { $pull: { 'contact.phone': { number: '+1786543589455' } } }
);

It will find document with the given _id and remove the phone +1786543589455 from its contact.phone array.

You can use $unset to unset the value in the array (set it to null), but not to remove it completely.