The challenge with qualifying spend is the same challenge with points: the process for awarding base points for stays is mature and reliable (because even in cases where mistakes are made, Marriott offer the missing stay form which will dispatch a Marriott employee to resolve the problem) but everything else (like hotel's giving special rates that include bonus points) is pretty adhoc. You are relying on hotels to understand the nuances of the Marriott program and report it correctly and be willing to resolve any issues you spot.

If you spend in a hotel's onsite restaurant that is ran by the hotel during a stay then you should earn points on that spend and it should count towards your qualifying spend but there's many different steps in the process where the hotel might make a mistake. If you've already made it to Ambassador status then you can try to leverage your Ambassador to resolve these issues for you (because your Ambassador can file a case with the hotel) but otherwise it's pretty hard to get them resolved because Marriott's customer support is not empowered to go off-piste to resolve issues, they're pretty much picking from a list of known scenarios and replying with a template.

I think the best way to ensure you get as much credit for your spend as possible is:

1. Confirm with the hotel that they operate their onsite restaurant (or any other venue you may spend at)
2. Ask that your purchases are associated with your room (ideally, charged to your room, but if not, ask the restaurant to make a note of your room on the receipt)
3. At checkout, ask to review your folio and confirm that all of the charges are recorded on it: if there are missing charges, ask for a note to be made on the folio about the additional spend (your folio is the source of truth, if it's not on the folio, it didn't happen)

After you've checked out and the points + spend have been posted (usually the next day) review and cross check (making sure to account for the taxes/fees which are not counted). If the total seems incorrect, reach out to your Ambassador, or, if not Ambassador yet, the hotel, and flag the specific entries that you do not think have been credited correctly.

4. Question your sanity, wonder whether spending your life auditing qualifying spend is the life you dreamed of for yourself