basejester

5.08 (4.09) How a Team Scores
(a) One run shall be scored each time a runner legally advances to
and touches first, second, third and home base before three men
are put out to end the inning.
EXCEPTION: A run is not scored if the runner
advances to home base during a play in which the third
out is made (1) by the batter-runner before he touches
first base; (2) by any runner being forced out; or (3) by
a preceding runner who is declared out because he
failed to touch one of the bases.

Delayed.
6.02 (5.07)(f ), (g), (i), ( j) Pitcher Illegal Action
a) Balks
. . .
PENALTY: The ball is dead, and each runner shall advance one
base without liability to be put out, unless the batter reaches
first on a hit, an error, a base on balls, a hit batter, or otherwise,
and all other runners advance at least one base, in which case
the play proceeds without reference to the balk.
APPROVED RULING: In cases where a pitcher balks and
throws wild, either to a base or to home plate, a runner or runners
may advance beyond the base to which he is entitled at his
own risk.

Definition of Terms
A BALL is a pitch which does not enter the strike zone in flight and
is not struck at by the batter. If the pitch touches the ground and bounces
through the strike zone it is a “ball.”

2.0 Force Out
. . .
Example: Not a force out. One out. Runner on first and third. Batter flies out. Two out. Runner
on third tags up and scores. Runner on first tries to retouch before throw from fielder reaches first
baseman, but does not get back in time and is out. Three outs. If, in umpire’s judgment, the runner from
third touched home before the ball was held at first base, the run counts.
 
4.09 HOW A TEAM SCORES.
(a) One run shall be scored each time a runner legally advances to and touches first,
second, third and home base before three men are put out to end the inning.
EXCEPTION: A run is not scored if the runner advances to home base during a
play in which the third out is made (1) by the batter-runner before he touches first
base; (2) by any runner being forced out; or (3) by a preceding runner who is
declared out because he failed to touch one of the bases.
 
7.09
. . .
(d) He fails to retouch his base after a fair or foul ball is legally caught before he, or his
base, is tagged by a fielder. He shall not be called out for failure to retouch his base
after the first following pitch, or any play or attempted play. This is an appeal play;

Assuming baseball, that's an incorrect call.  I don't remember the reference, but somewhere in rule 7.
 
He's leaving early from second base, and subject to being forced to return under some circumstances.  But not called out.   
 
Softball is different.  The runner is just immediately out.