Q: If I just missed a prayer and have to choose between making it up or joining the congregation for the current prayer, what should I do?
A: You should make up the prayer you just missed and then join the congregation if you can. Potentially missing the congregational prayer of the current prayer is not an excuse to void the order of prayer even if you have to pray it alone. Making up the prayer you just missed is a valid excuse for missing the congregation. If you are going to miss the current prayer’s obligatory time by making it up, then the order is voided and you are required to pray the current prayer and then the missed prayer. Source: Sharh al-Muntaha, Kashshaf al-Qina’