"The fly goes in the bottles."
Translation:La mosca va nelle bottiglie.
"Into" is probably the most appropriate here. "Into" signifies a terminal destination within an enclosure. For example, "he goes into the store" would signify that the store is the terminus of his going, the goal of the action, or the conclusion of motion/action. On the other hand, "he goes in the store" would signify that the store is not the terminus of his action, but only that it is either a transition or a location of a subsequent action, as in: "he goes in the store and buys some candy." The terminus of his going is the goal of buying candy. With the preposition "in", there is almost a waiting or an expectation of a subsequent action. However, with stative verbs you have to use "in" since there is no motion/action.
I'll have to think about this- but actually, I think that "go in" and "go into" are usually used in the same way. Going "into" has the further connotation of going further into something- or going into an enclosed area..
In slang, though, to "go" can mean to urinate- and since we're talking about "going in a bottle" in brings to mind a doctor's office.... so it just sounds better to say that the fly goes inTO the bottle- but I am probably being way too picky.
We have language issues (both English and Italian) that are far more important that this little point. Don't worry about it.
To add to Christopher's explanation, "into the bottle" to me simply emphasizes that at first it was outside of the bottle and then ended up inside, whereas "in the bottle" could mean it was already in the bottle or not. Consider changing the verb here from "to go" to "to fly" and perhaps it will make more sense, for example... "It flies into the bottle from outside." vs. "It flies around in the bottle." I'd say you could use "in" (or "inside") with both those sentences, but "into" only with the first one.