There are many prefaces. Not all of them even have that phrase in them. When they don’t noone will say amen. It is only the times it does people do and for no reason.
As for the “Amen”, I will admit sometimes I even catch myself about to say it. It becomes reflexive habit - and when you’re a good mimic (and apparently I am, from all I’m told) it’s even harder to not do it.
Normally, “through Christ our Lord” in a prayer is followed by an “Amen”. So yes, it’s a reflexive response.
Most people who are not brand new Catholics are not sitting there with a book of Propers in their hand following the absolutely correct responses. They are responding from memory or from the reflexive response when they hear something that normally triggers an Amen. I don’t think it’s a big deal, as obviously there is no intent to be irreverent or to interrupt the priest.
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