Apple Store is telling me my MacBook Pro problems might not be covered by warranty?

Dirt can get inside the system through the keyboard. So it may really have been your fault.

 

Dirt (and food) is pretty much non-conductive, so even if crumbs did manage to make its way into the computer, the only thing it should effect is the fan (as it's mechanical) and the computer will turn off before it overheats, so at most it should be a $7 fan.

The problem the OP has is that if Apple can determine that any portion of the mac is not covered due to how the computer was treated, that invalidates the entire warranty, and the OP will have to pay $1200 to have the entire machine fixed outside of warranty. And Apple comes out $1193 ahead at OP's expense.

My suggestion is to clean the mac completely so externally, it looks brand new. Then take it back in.

 

Bingo! You should have had that in your OP, because that's a vital piece of information to your story. Because you didn't, it gives me the impression that you're "stacking the deck," so to speak, to garner sympathy for your issue, and attempt to get some suggestions on how you can get the damage fixed for free. Not saying that actually is what you're trying to do here ... it's just the perception that I've been given as a result of how you've gone about relaying the information on your system here.

How much was paid that time? My guess is that there is a record of that repair in their system, which states water damage was the cause, and which is probably the reason why they're saying the current issue has a 50% chance of not being covered by warranty. This is because the current issue stands a chance of being caused by the previous water damage.

If they put the repairs in as warranty service, then consider yourself lucky, and a lesson well learned/earned. If they charge you for it, consider it a very expensive lesson learned.

The moral of this story? Don't eat or drink near your laptop.

 

Back it up, too, while you're at it. Nobody should be left without a current backup, unless they simply don't care about the data on their computer. It's not a matter of if you lose your data but when.