Learn French: Il y a une goutte d'extrait dans le flacon. - There is a drop of extract in the flask.

Because une goutte is an expression of quantity. Just like with beaucoup de or un peu de, nouns following a specific quantity take de (or d') without a definite article. You would only use de l'extrait if you were referring to a specific extract that was already mentioned (meaning a drop of the extract).

What is the difference between un flacon and une bouteille?

While both mean 'bottle', un flacon refers to a small bottle, vial, or flask used for perfume, medication, or scientific liquids like this extract. Une bouteille is typically larger and used for everyday beverages like water or wine.

If we already know we are talking about the flask, could we use dedans here?

Yes! Dans is a preposition and must be followed by a noun, as in dans le flacon. If the flask was already mentioned in a previous sentence, you could replace the whole phrase with the adverb dedans (inside / in it) and say: Il y a une goutte d'extrait dedans.