Why does the Torah refer (albeit briefly) to the lack of water in Refidim and the miracle, but not to that of Marah or to the miracle of the Manna in Midbar Sin?
Ramban: Because, as opposed to the latter two, which were minor incidents, the current one was a major one, incorporating their testing Hashem, the naming of the place Masa u'Merivah, the sanctification of Hashem's Name when He produced water for them and the ensuing battle with Amalek.
Elef ha'Magen: Refer to 33:8:151:1. This was a Siman that Yisrael will be stricken and afflicted, and then water will exude (Torah in exile).
Why were they suddenly short of water?