As MSPeconomist notes, there are technical reasons why the second room didn't generate Points for you. Here are the Terms and Conditions explaining the which Qualifying Charges generate Points (emphasis mine):

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Charges incurred during a stay in a guest room at a Participating Property by a Member on his/her folio and up to two (2) additional guest rooms, including, without limitation, charges for:

A. Qualifying Rates for Stays;
B. Food and beverages (excluding alcoholic beverages where prohibited by law) and may exclude charges incurred at outlets that are not managed or operated by the Participating Property;
C. Direct-dialed in-room telephone and direct-dialed in-room fax;
D. In-room movies and video games;

provided the Member provides his/her Membership Number at the time of reservation or at check-in, stays in one of the reserved guest rooms, and pays for the charges.
Source: https://www.marriott.com/loyalty/terms/default.mi#earn
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Regarding the bolded conditions, it sounds like you meet the last two. Did you provide your membership number on the second reservation or at check in? If you did, you should be getting Points.

As you've discovered with this thread, clarity matters. Many of us assumed you were talking about Nights because you specifically used that word and the response you quoted addressed that fact.

If you did provide your membership number as required for that second room, let Marriott know and ask for those Points. Don't use the term Nights because that will likely generate a similar response to what you already received.

An easier way to resolve this would be to call the hotel during normal business hours (wait until Monday) and ask them to issue points for the second room. A call will be quicker than waiting for an email response. Plus, if the person starts mentioning the restriction regarding Nights, you can immediately tell them you're only looking for Points.