“en” replaces “roses”, so you can’t use both in the same sentence, except with a comma:

Il en a acheté une douzaine, de roses

But this will mostly be used in an oral conversation, when you start using “en”, and realise the person in front of you is not sure of what you are talking about, or if you simply want to emphase it.

The correct way to use “en” is, as you said first:

Il en a acheté une douzaine

Side note
You may also see something like this, which has not the same meaning:

Il en a acheté, des roses

which emphasis the high amount of roses, meaning “il a acheté beaucoup de roses”.

When putting the word ‘en’ into a sentence, you must make sure to place it before the verb AND the number.

Eg. J’ai trouvé une pomme sur la terre. —- J’en ai trouvé UNE.

So as the first answer stated, you’re first one was correct, and I find that it’s the one that sounds the best.

"En" replaces the noun.

Il a acheté une douzaine de roses == Il en a acheté une douzaine

Of course, you have to know that you’re talking about roses. Usually, context has been established by a previous sentence:

Il est parti chercher des roses chez le fleuriste. Il en a acheté un douzaine.

As Random said, orally you can find things like "Il en a acheté une douzaine, de roses". Typically this can happen when you realise half sentence that you didn’t provide context, so you just give it afterwards, or you thought you were being clear, but there is a possible confusion so you need to clarify.

You can also say this to emphasize :

Il en a acheté, des roses.

He sure did buy a lot of roses.

Other ways of using "en" :

Il a acheté une rose == Il en a acheté une

Il a acheté des roses == Il en a acheté