Template format error: Unresolved resource dependencies

!Ref only works for Logical ID that exists within the template. That doesn't mean that you can't reference an existing security group, that just mean that you'll have to reference it in some other way. For your particular use case I suggest you pass the security group as a stack parameter like so:

Parameters:
  KeyName:
    Default: TestKeyPair
    Description: Name of an existing EC2 KeyPair to enable SSH access to the instance
    Type: AWS::EC2::KeyPair::KeyName
  SSHSecurityGroup:
    Description: SecurityGroup that allows access to the instance via SSH
    Type: AWS::EC2::SecurityGroup::Id
Resources:
  Dev:
    Properties:
      ImageId: ami-4e79ed36
      InstanceType: t2.micro
      KeyName: !Ref 'KeyName'
      SecurityGroups:
        - !Ref SSHSecurityGroup
    Type: AWS::EC2::Instance

On the stack creation you just have to pass the SSH Security Group in the appropriated field.

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That being said, you won't have a much dynamic setup if you do it this way. You should either define the security group within this template and reference it directly (using !Ref), or you could create a template that manages all security groups and use the Export/Import feature of CloudFormation to reference the security groups between stacks.