I've noticed a distinct correlation between getting an inadequate room and a late arrival. Every time I have gotten one, I have arrived hours after check in and typically during the summer where there is high occupancy.
When Marriott sends out the pre-arrival, I always indicate that I'm arriving at 4pm now and I do try to arrive close to check in if possible, so if there are problems in the unit, I can ask to be moved, before other options are occupied.
I've had several stays at Marriott managed resorts where the rooms have issues. I've had a couple with foul odors in the room. Like a critter died, maybe in the duct work? If others arrived earlier and had the same complaint, it's likely that they got moved to another room (probably your assigned room, since you haven't arrived yet) and you get stuck with that subpar room.
I've also arrived to a partially cleaned room, but was able to get moved.
I had a recent short stay where I had to arrive a day late and even though I notified the resort that I wasn't arriving until the next day, I received a call from maintenance asking to come in and do a significant repair after I arrived. How lame is that? They had a heads up that I wasn't going to occupy the room and yet somehow they couldn't do the repair during that 24 hours? Of course, I refused. Considering it appeared that there was black mold under the sink cabinet, they probably shouldn't have let the room be occupied at all. Did management care? Not at all.
In June, at another Marriott affiliated resort, I was "bumped" from the room I was assigned for a two week stay. I know because in that particular resort, some owners own fixed weeks and units. This was an exchange and showed that information on my confirmation and prior to arrival I called the resort to confirm my reservation and the front desk agent "let it slip" that I was in that unit for both weeks (which they typically don't do because of this exact issue). I was feeling pretty comfortable about arriving late knowing that my preferred location was assigned. I arrived about 9:30 pm to find that I no longer was assigned to the room on my confirmation, but that I also was going to need to change rooms after the first week. There was already another party at reception with a loud complaint about their room(s) assignment. They were supposed to have adjoining rooms in a lock off, but were instead assigned to lock offs in separate units. The front desk agent lied to me when I asked if the assigned room was on an upper floor, so I took the keys and drove to the unit only to discover that he lied. So I drove back to reception and waited in line again. They were still surprisingly busy for after 10pm. The agent who helped me originally was not present and the new agent was not very hospitable. I'm a very understanding person and I never lose my temper and yell loudly to create a scene, but I understand the OP's frustration of arriving tired and being lied to; it's not the way to run a hospitality business, even if the customers are somewhat hostages as timeshare owners/exchangers, rather than retail customers. Exchangers, may become owners, so I don't know why it seems okay to treat them as second or third class when it comes to checking in. I didn't feel it was important to mention that I was told that I was assigned to a particular unit, but if the management hadn't decided to bump me, they wouldn't have had to deal with additional complaints and probably unintentionally encouraged the party who got my unit to complain in the future. I think most people at this resort prefer to be on second floor rather than the first and I think that was probably why I got "bumped". Long story short, sometimes the resort creates avoidable issues and should try to minimize this from the start.
Marriott, handled the OP's situation poorly at check in, as no one likes to lied to, on top of being tired from travel and getting a subpar room. Sometimes there are conditions which are hard to avoid and hospitality employees should be trained in how to handle these situations. I'm glad to hear that the manager took OP's concerns seriously and provided a fair compensation.
In more than a half dozen instances where there's been an issue with a unit at check in, I've only once received a comp, 50k bonvoy points. I guess I need to learn how to complain better, but truly, I'd just prefer for the management to be honest and acknowledge the issue, instead of making it seem like I'm the problem. It's vacation, no one wants to deal with problems on vacation, much less create them