Preface: I watched the game listening to the Cincinnati feed, so I don’t know what Gary Cohen said during the broadcast:

The official rules regarding illegal substitutions has already been posted and is posted again below.

1) Patterson (8th) was the scheduled batter
2) Ross (9th) actually went up to hit and made an out
3) Patterson then came to bat
4) Randolph protested that the Reds batted out of order before the next pitch.
a. In this case, the proper batter (Patterson) is called out, and the next proper batter in turn comes to the plate
5) Had Randolph NOT protested, and a pitch been thrown to Patterson, then the following would have occurred
a. Ross’s at bat would have been legalized, and his out would have stood.
b. The new proper batter is the one after the now legalized Ross, which would have been Ryan Freel (1st)
c. Had Patterson instead completed the at-bat and reached safely, the Mets could have then protested that Patterson batted out of turn and had him called out.
d. Had Patterson completed the at bat and made an out, then the Mets would also say nothing. The Reds would likely send Freel up next, whereas once Patterson’s at bat was legalized, the next proper batter would have been Ross (since Patterson’s at bat would have been legalized, the next proper batter is the one after Patterson, namely Ross). If Freel gets on safely, they could then protest his at bat and have him called out.

See the text of the relevant rulebook below, including the official examples which flesh the ruling out:

6.07 BATTING OUT OF TURN.
(a) A batter shall be called out, on appeal, when he fails to bat in his proper turn, and another batter completes a time at bat in his place.
(1) The proper batter may take his place in the batter’s box at any time before the improper batter becomes a runner or is put out, and any balls and strikes shall be counted in the proper batter’s time at bat.
(b) When an improper batter becomes a runner or is put out, and the defensive team appeals to the umpire before the first pitch to the next batter of either team, or before any play or attempted play, the umpire shall (1) declare the proper batter out; and (2) nullify any advance or score made because of a ball batted by the improper batter or because of the improper batter’s advance to first base on a hit, an error, a base on balls, a hit batter or otherwise.
NOTE: If a runner advances, while the improper batter is at bat, on a stolen base, balk, wild pitch or passed ball, such advance is legal.
(c) When an improper batter becomes a runner or is put out, and a pitch is made to the next batter of either team before an appeal is made, the improper batter thereby becomes the proper batter, and the results of his time at bat become legal.

(d) (1) When the proper batter is called out because he has failed to bat in turn, the next batter shall be the batter whose name follows that of the proper batter thus called out;
(2) When an improper batter becomes a proper batter because no appeal is made before the next pitch, the next batter shall be the batter whose name follows Rule 6.07 56
that of such legalized improper batter. The instant an improper batter’s actions are legalized, the batting order picks up with the name following that of the legalized improper batter.

Rule 6.07 Comment: The umpire shall not direct the attention of any person to the presence in the batter’s box of an improper batter. This rule is designed to require constant vigilance by the players and managers of both teams.
There are two fundamentals to keep in mind: When a player bats out of turn, the proper batter is the player called out. If an improper batter bats and reaches base or is out and no appeal is made before a pitch to the next batter, or before any play or attempted play, that improper batter is considered to have batted in proper turn and establishes the order that is to follow.
APPROVED RULING
To illustrate various situations arising from batting out of turn, assume a first-inning batting order as follows:
Abel-Baker-Charles-Daniel-Edward-Frank-George-Hooker-Irwin.
PLAY (1). Baker bats. With the count 2 balls and 1 strike, (a) the offensive team discovers the error or (b) the defensive team appeals. RULING: In either case, Abel replaces Baker, with the count on him 2 balls and 1 strike.
PLAY (2). Baker bats and doubles. The defensive team appeals (a) immediately or (b) after a pitch to Charles. RULING: (a) Abel is called out and Baker is the proper batter; (b) Baker stays on second and Charles is the proper batter.
PLAY (3). Abel walks. Baker walks. Charles forces Baker. Edward bats in Daniel’s turn. While Edward is at bat, Abel scores and Charles goes to second on a wild pitch. Edward grounds out, sending Charles to third. The defensive team appeals (a) immediately or (b) after a pitch to Daniel. RULING: (a) Abel’s run counts and Charles is entitled to second base since these advances were not made because of the improper batter batting a ball or advancing to first base. Charles must return to second base because his advance to third resulted from the improper batter batting a ball. Daniel is called out, and Edward is the proper batter; (b) Abel’s run counts and Charles stays on third. The proper batter is Frank.
PLAY (4). With the bases full and two out. Hooker bats in Frank’s turn, and triples, scoring three runs. The defensive team appeals (a) immediately, or (b) after a pitch to George. RULING: (a) Frank is called out and no runs score. George is the proper batter to lead off the second inning; (b) Hooker stays on third and three runs score. Irwin is the proper batter.
PLAY (5). After Play (4)(b) above, George continues at bat. (a) Hooker is picked off third base for the third out, or (b) George flies out, and no appeal is made. Who is the proper leadoff batter in the second inning? RULING: (a) Irwin. He became the proper batter as soon as the first pitch to George legalized Hooker’s triple; (b) Hooker. When no appeal was made, the first pitch to the leadoff batter of the opposing team legalized George’s time at bat.
PLAY (6). Daniel walks and Abel comes to bat. Daniel was an improper batter, and if an appeal is made before the first pitch to Abel, Abel is out, Daniel is removed from base, and Baker is the proper batter. There is no appeal, and a pitch is made to Abel. Daniel’s walk is now legalized, and Edward thereby becomes the proper batter. Edward can replace Abel at any time before Abel is put out or becomes a runner. He does not do so. Abel flies out, and Baker comes to bat. Abel was an improper batter, and if an appeal is made before the first pitch to Baker, Edward is out, and the proper batter is Frank. There is no appeal, and a pitch is made to Baker. Abel’s out is now legalized, and the proper batter is Baker. Baker walks. Charles is the proper batter. Charles flies out. Now Daniel is the proper batter, but he is on second base. Who is the proper batter? RULING: The proper batter is Edward. When the proper batter is on base, he is passed over, and the following batter becomes the proper batter.

Baker is a mess, so I wouldnt be surprised if he made a few flubs.

using Heilman and Sosa is both games of the double header is an interesting way to use the pen, but I guess those guys were good to go.