Desencallar literally means "to refloat" or "to unground" a ship that is stuck. It's a vivid and somewhat nautical term that isn't commonly found in everyday song lyrics.
In this song, it's used metaphorically in the line "Nos faltó desencallar el fin" (We failed to unground the end). Here, it implies an attempt to salvage or rescue a relationship that was stuck or heading towards an inevitable end, suggesting a desire to change its course before it was too late.
"Entre Sobras y Sobras Me Faltas" turns on a single pun: sobrar (to be left over) against faltar (to be missing). Antonio Orozco tallies everything a relationship had too much of against everything ordinary it never got to keep. He opens with the missing half: "Nos faltó una noche de franela" [We missed a flannel-pajama night], the plain comfort of an evening in rather than any grand gesture. The chorus makes the arithmetic explicit — "Y sobraron las quinientas veces que dijimos que no" [And the five hundred times we said no were extra] — proof that a relationship can drown in refusals and arguments while still running short on the small, everyday things that would have kept it going.