Tnejn is the "long form" and is used if it stands on its own, i.e. without noun. {Kemm-il ġimgħa? Tnejn biss.}

Żewġ is the "short form" and is used with nouns (plural) of more than one syllable.
{Għandi żewġ ħuti subien.}

Żewġt is the " t-form" and is used
1. with nouns (plural) of one syllable. The noun is preceded by a vowel 'i' if it begins with a consonant. {Għandi żewġt itfal.}
2. In case of a (semitic) noun of more than one syllable and beginning with a vowel it is used as well. {għaxart ilsna }

These are the rules.
According to this rules "żewġ kafè" would be the correct form however,
"Tnejn kafè" is regarded as fixed expression and thus an exception (historical reasons?).
There might more exceptions yet I don’t know for sure.