Learn Spanish (Latin America): A lo mejor tenemos que volver a alinear la secuencia. - Maybe we have to align the sequence again.

This is a major exception for probability phrases in Spanish. While words like quizás and tal vez often trigger the subjunctive, a lo mejor (maybe / perhaps) always takes the indicative. Even though you are expressing doubt about having to realign the sequence, you must use the indicative tenemos, never the subjunctive tengamos.

How does volver a alinear mean "align again" if there is no word for "again" in the sentence?

In Spanish, the most natural way to say "to do something again" is using the formula volver a + [infinitive]. Here, volver combines with the infinitive alinear (to align) to mean "to re-align" or "to align again." While you could technically say alinear la secuencia otra vez, this volver a structure is much more native-sounding and common.

Is it normal to stack verb phrases together like tenemos que volver a alinear?

Yes, it is completely normal! This sentence links two common verb formulas together. First, tener que + [infinitive] gives us tenemos que volver (we have to return/do again). Then, volver a + [infinitive] requires the final action, giving us volver a alinear. They chain together perfectly seamlessly.

If I actually wanted to use the subjunctive verb to express this same doubt, how would the sentence change?