[Vuejs]-Element focus jumping on setting it to empty

You could try simply reset focus manually using focus() method on the ref object.

You will need to add ref attribute to the input.

   <input ref="applyToAll" id="applyToAll" class="custom-control-input" type="checkbox" @change="applyToAll"/>

   <div v-for="(data,index) in users">
      <div :key="index">
          <input v-model="data.contactInfo.phoneNumber">
      </div>
   </div>

And your applyToAll method:

applyToAll() {
      if (this.appliedToAll) {
        const copiedPhone = this.users[0].contactInfo.phoneNumber;

        this.users[1].contactInfo.phoneNumber = copiedPhone;
        this.users[2].contactInfo.phoneNumber = copiedPhone;
      } else {
        this.users[1].contactInfo.phoneNumber = '';
        this.users[2].contactInfo.phoneNumber = '';
      }
      this.$refs.applyToAll.focus();
}