Well, it’s the fact that a hotel that has so much CIA? stuff is run by one guy who does heroin & so really is not reliable. They would have sent more than one agent to make sure it was cleaned up if that were the case. I think there had been a few more employees & Miles killed them & they are in the maintenance shed. I think he did this because he thought Flynn would be the only guest. Thus, let him check in, find the money, then either kill Flynn to or just take it with the master key while Flynn slept. I also think that Miles got a job at the El Royale in hopes of finding the money, so he did legit work there (maybe drafted in between?) & understand how it worked & what the point of it was.
Again, it’s far fetched & I need a rewatch but stuff just didn’t add up in the way the actors behaved which made me think they were given knowledge to play off of in how to behave towards the others even if it’s subtle.