Dead ball foul, then live ball foul?

[stegenref]

Last night during a 7th grade game, we had the following situation occur. I was working the HL position, and the defense jumped offsides, so I threw my flag and blew my whistle, but the ball was snapped before I was able to run out there and blow my whistle enough times to stop the play...they didn't get very far at all...didn't even make it to the handoff. The LJ on the other side of the field threw his flag too. We both came together in the middle of the field to talk to the WH, who asked what we had. I told him I had encroachment on the defense and the LJ told him he had an illegal formation because there were only six men on the LOS. The WH then penalized both teams. Later, during a time-out, I was asking him how there could be a dead-ball foul followed by a live-ball foul, because how could there be a live-ball foul if the ball was never technically live. He said because I took too long to blow the whistle, so I didn't kill the ball. I told him I thought the ball was "dead by rule" and that the whistle doesn't necessarily kill the ball....the ball was dead as soon as the defense encroached. He told me that I didn't stop the play soon enough, so the ball became live, so there was a live ball foul. That just doesn't seem right to me.