Do yourself a BIG favor, and don't listen to fans. YOU place the ball where YOU decided it should be placed. Once you DECLARE a spot, stick with it, but don't be in such a rush to declare it, until YOU are certain where YOU want it to be.
Today, it's not uncommon that someone (or multiple external people) will see a different "spot" on EVERY play that goes OOB. Everyone is entitled to their opinion, but yours is the only one that matters. Best to be careful about deciding on it, and confident in your decision, although as suggest above, it's a smart idea to visually check with either/both the Referee (trailing the play) or a Judge in front of the play on your side/sideline before finalizing YOUR decision and "placing" the ball.
If there should be any indication of a different spot by another OFFICIAL, converge with that official and collectively agree where exactly the ball should go BEFORE placing it. If leaving YOUR spot, leave a beanbag marking it.
Regarding example 2, Go to the Referee, advise him what happened. The holder "killed" the ball when he pitched the ball with his knee still on the ground. Everything that happened after that, happened with a dead ball.
Not blowing the whistle to stop play was a mistake that can be corrected, allowing it to go uncorrected is a tragedy. Go immediately to the Referee and advise him what happened, and what you SAW.
After confirming what you SAW, the Referee must then signal; no score, the ball was dead at the spot, the down ended and it's either 1st & 10 the other way, or a kickoff.
It would be a real good idea for the Referee to go to the offensive Coach, at his sideline, and explain what happened and the relevant rule.