Update: The hotel and Seaworld both contacted me and agreed it was unclear and will be working to fix the pdf. Marriott went above and beyond to make ammends even after I told them I just wanted them to fix it so no one else makes the same mistake. I wasn't even mad at Marriot because it was Seaworlds web site. I just felt they should know. The guy was so nice about it that we will be staying there a lot I think.
Seaworld comped us some quick queue tickets for our next visit. So kudos to both Seaworld and Marriot in this situation.
Just as an FYI, he said that this is only the second time that they have ever run out of the passes. Of course, it was a holiday weekend which is why. He was also very glad I emailed because their quick queue passes with the room has only been added less than a year ago. Unlike Universal, where it's guaranteed with a room key, it's not at Seaworld and it's not worded well in all areas. So this is something they will be looking into more.
For anyone going, I wouldn't worry too much unless it's a holiday. He really made it sound like it was rare. We are going to go back next weekend and try it again.