It is a sports metaphor.
Umpires (or referees in some sports) make "calls." They decide whether a ball was in or out, whether a player has done something against the rules, whether or not a penalty needs to be applied. Each of those decisions (or any similar decision) is a "call"
Sometimes a call is easy - the ball was nowhere near where it was supposed to go. But sometimes it is hard to make that decision (due to things being very hard to see, or where the rules are complex). That is a "tough call."
In casual conversation a "tough call" is that type of decision, one where it is difficult to know and make the correct decision.