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Why is it that someone who is fully capable of producing a sound foreign to their own language has trouble using that sound in languages that do use it?
For example, let's say that an English speaker can perfectly pronounce the alveolar trill [r]. Why might they have trouble pronouncing that sound in words?
One point to add is that ability to produce a word in isolation does not translate into ability to produce that word faithfully in extemporaneous running speech. Fluency in speaking requires you to be able to pronounce words accurately without having to concentrate on pronunciation in itself. Your working memory will already be taxed by demands on forming ideas, selecting the appropriate grammatical constructions, lexical access, the emotional effect you are trying to impart, etc. Fluency requires correct pronunciation under pressure. A viable strategy for most L2 speakers is to settle on a bad pronunciation but an understandable message that is not delivered haltingly.
The following reference may help to understand why trills are difficult to produce in certain contexts:
Solé, M.J. 2002. Aerodynamic characteristics of trills and phonological patterning. Journal of Phonetics 30, 655-688.
I'm not sure I know exactly what you mean - for one thing, it's difficult to define what a "perfectly pronounced" alveolar trill would be, because every language that has the phoneme /r/ realizes the phone [r] in a slightly different way - but I think the answer probably has to do with coarticulation, which refers to the phenomenon in which speech sounds (segments) have their pronunciation / phonetic realization influenced by adjacent segments, as well as the process of transitioning between two different segments. Although we analyze speech as a series of discrete segments, it's certainly a continuum on the surface, and therefore all phones within words are at least somewhat affected by coarticulation.
To return to your specific example, all this means that a person who can pronounce [r] well in isolation may still have trouble pronouncing words containing the sound, because they are unaccustomed to 1) the act of transitioning between [r] and another sound, and 2) the subtle ways that adjacent sounds affect how you pronounce [r].
