Don't shoot him with his head down (??)

[Scorch]

When a deer puts his head down, they go into "flight" mode.
They have let their guard down and are tense, alerted to jump, toward any perceived threat.
If they hear a "click", or "pop", before the actual pill hits, they may jump the shot.

Actually, if a deer is in "flight" mode, they won't put their head down because it makes them more vulnerable. They will only lower their head if they feel safe enough to do so. They are not stupid.
If they hear a "click", it's because you made some other noise before the shot, not because the gun made noise when you shot. Bullets are supersonic, i.e. travel faster than sound. Even a deer's keen reaction time is going to be 1/10th of a second, and in that time a bullet can travel 75-100 yds (depending on initial velocity), whereas sound will only travel 35 yds in the same amount of time. If a deer moves between the time you fired and the bullet hit, it likely because they saw movement when you fired.

Even if you are shooting a muzzleloader, the bullet is typically still supersonic unless you are shooting large caliber patch and ball.

In the end, I don't know why a guide would tell anyone not to fire when the animal's head is down. I keep reading the replies hoping someone knows.

[Yithian]

I was speaking of other deer, twigs, safety's etc. Not the actual bullet.
I can't think of the proper wording other than "flight" but lets just say, they tense up bad, ready to move asap. LOL
Comfortable enough to put the head down, does not mean they are comfortable.
It's a necessity they must do to eat.