There are a dozen pens on the table.
Although this seems odd, if we go back to basic English and diagramming, we will see that "dozen" is used as a "definite numeral adjective" here, "a" is an "adjective article", and "pens" is the noun.
When used with the indefinite article, certain numeral adjectives require the singular version of the indefinite article (a/an) in front of it (a few, a dozen, a hundred, a million, a billion, etc) instead of a plural indefinite article (some) or no article at all in English, even though they are describing something plural.
A dozen apples in the tree...
A billion stars in the universe...
Although "apples" and "stars" are plural, they are referred to as singular objects when used with these definite adjectives. However, "apples" and "stars" ARE still the objects here.
If we leave out the objects,
A dozen in the tree
A billion in the universe
then, and only then, do these numeral adjectives, become nouns, which must have another noun to refer to. I can't say "He went to the store," without knowing who "he" is. There is a billion in the universe. A billion what?