"Listen" actually can have either 5 or 4 sounds, but the difference is not important in English. So don't worry too much about it.
Both [ˈlɪsn] and [ˈlɪsən] are possible pronunciations: they are phonetically different because in the first one, the consonant sound [s] is followed directly by the consonant sound [n], while in the second, there is a brief vowel sound [ə], called schwa, between them.
If we say the word as [ˈlɪsn], the consonant [n] is syllabic (unlike the [n] in a word like "snail") and an optional way to mark that a consonant is syllabic in the International Phonetic Alphabet is to put a short vertical line below it, like this: [lɪsn̩].
Even though syllabic consonants can occur in some English words, their use is optional: a syllabic consonant can always be replaced by a schwa followed by a non-syllabic consonant without changing the meaning of a word. Since there is no contrast, a "phonemic" transcription (a transcription that only shows contrasts that can make a meaningful difference) will generally include the schwa: /ˈlɪsən/.
By convention, slash marks are supposed to be reserved for phonemic transcriptions, whereas phonetic transcriptions are supposed to be surrounded by square brackets like [lɪsn̩].
Here are references I provided when answering Are ə before l/m/n/r optional? on ELU Stack Exchange: two blog posts by the phonetician John Wells:
In the first of these, Wells says
Syllabic consonants are never categorically required in English. There is always an alternative pronunciation available, with ə and a nonsyllabic consonant.