Inadvertent whistle in the end zone question--

[kfo9494]

Last night, I had a Jr high game with a new, but eager, official.
During the second quarter we had an interception in the endzone. The player started to run but the official blew his whistle and gave a beautiful touchback signal.
I knew it was an IW and told both coaches (not sure if they even knew what a IW was) and placed the ball on the twenty yard line and gave it to the team that intercepted the ball since the ball became dead behind the endzone. Even gave the team a choice of result or replay. And just knew I was correct. I would have even done the same thing on a friday night game.
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Today, I just read the rule book concerning IW and noticed that in the case book 4.2.3 Situation D it says it should be a safety if the team takes the result of the play. The play in the case book deals with the momentum rule where a player intercepts on the 2 yard line and then goes into the endzone. It says it is a safety if the team takes the result of the play.
How can this be-- It Rule 8-5-2 under the exception the momentum rule says if the ball becomes dead in the end zone it belongs to the team last in possession at the spot of the interception.
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Does this seem like the rule contradict each other or am I missing something? And did I blow the result of the IW last night?