In these situations, having low profile on a shinobi especially is a godsend.
There is also the chance you will get activations from directions you were not prepared for, this is especially true on supply runs, where it is not at all uncommon to be bracketed on 3 sides by pods that are around 10 aliens each. In these situations, you are not going to alpha everyone in one turn. It's in fact basically standard for supply raids, landed UFO's and HQ assaults.
Not sure how much you've played, or how far you've played, but missions with 20+ aliens activated at once are not uncommon.