In phonemic analysis, we say that a single phoneme, such as /l/, can often be pronounced in different ways, and we call each of these variants an allophone and show it in square brackets .
A classic example of allophones is clear and dark /l/. In English, a dark /l/, which we show as [ɫ], occurs at the end of a word such as full; but a clear /l/, which we show as [l], occurs at the start of a word such as like. Note that you can predict which one occurs according to its position in the word, which means they must be allophones, not different phonemes.
Between two vowels, such as in really or silly, British English has [l] (a clear /l/) but American English has [ɫ] (a dark /l/). Note that you can still predict which one occurs so long as you know which variety of English is being spoken.
What about /l/ in Malay? An interesting issue here is that a dark /l/ occurs between vowels only for words with an obvious Arabic origin, particularly Allah. This poses a problem for phonemic analysis, and we might even have to conclude that clear and dark /l/ are different phonemes in Malay.