I think, this varies from scene to scene. For example, I was recently watching Modern Family and in a scene, Jay & Gloria's son is shown starts crying, when his mother is putting him in his baby-car and stops crying when she pulls him out. Similarly in one episode the baby pukes as soon as someone talks of Gay-marriage. This is shown 3 times. What's similar in both scenes is that the camera is never close enough on the baby so that you can't notice baby's face in any scene. This means that while shooting the baby didn't do anything. they just played sound and made us feel that way. I am sure we all have seen many similar scenes. So it can be assumed that in cases where we don't see baby's face clearly, there is nothing happening with the baby at all.
But in my opinion and it's a personal opinion, the possibility of deliberately making a baby cry for a scene could not be denied. As I have seen in many movies, (not necessarily Hollywood) where an actual crying baby is shown. OP is right that it is highly unlikely that the producers will wait for the infant to start crying. It is unrealistic since the scene might require many retakes.
Now you might think why would the parents allow their baby to be made cry. Well, first of all, think why did they allow their infant to be used in a movie production at all.
In California, according to the law, any child as young as only
15 days can be used in a shooting. Surprisingly in many other
states, there is no minimum age at all.
Check this link for details.
As far as I know a baby with 15 days of age, needs a lot of rest and they sleep most of the time. Any parent's biggest concern is to pacify their crying babies, let alone the thought of deliberately making them cry, but still it is done. Why ? The same link states.
According to a SAG spokesperson, infants are typically hired as
"background actors" and receive a day rate of $126. If an agent or
parent bargains for the child to be paid as a principal performer, the
rate increases to $737 per day.
I don't think, it can be denied that kids are deliberately made to cry in some scenes.