In principle, there is no Qada for missed Sunnah Salaah. However, the Sunnats of Fajr are emphasized in the Hadith. Rasulullah (SAW) said ?do not leave out the two rakaats of Fajr (Sunnats) even though the horses trample upon you?.
Therefore according to Shariah, the sunnats of Fajr will be read only if it has been missed together with the Fardh. If the sunnats were left out due to joining the farz jamaat, the sunnats will not be read (Tahtaawi, Shaami)
And Allah Knows Best
and Allah Ta’ala Knows Best
Mufti Ebrahim Desai