Seasons has to do with the broadcast of a show, it doesn't necessarily always equate to 12 episode or how ever long each one is per season. It's just how many episodes or story arcs happen while the current season is on air before they stop it and prepare to make the next one.
Arcs has to do with the story. Wikipedia defines a story arc as:
A story arc is an extended or continuing storyline in episodic
storytelling media such as television, comic books, comic strips,
boardgames, video games, and in some cases, films. On a television
program, for example, the story would unfold over many episodes. In
television, the use of the story arc is much more common in dramas
than in comedies, especially in soap operas. Webcomics are more likely
to use story arcs than newspaper comics, as most web comics have
readable archives online that a newcomer to the strip can read in
order to understand what is going on. Although story arcs have existed
for decades, the term "story arc" was coined in 1988 in relation to
the television series Wiseguy, and was quickly adapted for other uses.
The way to tell the difference between the two is how they are broadcast and how the story continuity flows from episode to episode. There could be many story arcs in a single season of an anime, or there could be many seasons in an anime that only has one overarching story arc.