Monday Morning QB

1st-10 NYG34, 3:51 D. Rhodes rushed left for 6 yard loss
Timeout #1 by NYG at 03:45
2nd-16, NYG40 3:45 D. Rhodes rushed to the left for 3 yard gain
Timeout #2 by NYG at 03:38
3rd-13, NYG37 3:38 P. Manning passed to D. Clark down the middle for 14 yard gain
1st-10, NYG23 3:01 D. Rhodes rushed to the right for 6 yard gain
Timeout #3 by NYG at 02:43
2nd-4, NYG17 2:43 D. Rhodes rushed to the left for 2 yard gain
3rd-2, NYG15 2:00 J. Addai rushed to the right for no gain
4th-2, NYG15 1:16 A. Vinatieri kicked a 32-yard field goal
Indianapolis - 1:12 IND kicked off, C. Morton returned kickoff for 16 yards
1st-10, NYG23 1:12 E. Manning incomplete pass down the middle
2nd-10, NYG23 1:06 E. Manning passed to J. Shockey to the right for 12 yard gain
1st-10, NYG35 0:57 E. Manning passed to A. Toomer to the right for 16 yard gain
1st-10, IND49 0:30 NYG committed 5 yard penalty
1st-15, NYG46 0:17 E. Manning incomplete pass to the left

I do not know NFL rules, but when watching the game last night I was pretty sure the Giants botched it. After IND gets a first down at on the play at 3:38 they dont call their last timeout. I am ok with that. But then on first down the Colts run for 6 yards. The play starts at 3:01. I dont know how long a 6 yard run takes but i will assume it wasnt more than 6 seconds (since thats how long the first play listed above took). That means the first down play ended at 2:55 and they didnt take a timeout until 02:43. At which point the Colts run a second down play and then let the play clock take them to the 2 minute warning. If the Giants took their timeout immediately after the first down play, the Colts would have had to run a third down play before the 2 minute warning. Then they kick a FG on the first play after the 2:00 warning. Then the Giants get the ball back with something like 1:54 left, not 1:12.

I thought this was the case last night, but I wasnt sure. So i checked the play by play and I still think that I am correct. How are NFL coaches making these mistakes?