When Matt tells Sam about the blood stains he found in the storeroom, he asks Sam if he noticed anybody that might have left them. Sam said that he didn't, but he had been keeping a sharp eye out because of the shooting the night before. But that night, Kitty brought the wounded man from the storeroom, into the bar and up the stairs to her room. The saloon was packed with customers, and Sam would have been at the bar, or bringing drinks to someone at a table. Given the blood trail Matt and Festus found outside, and in the storeroom, even if Sam didn't notice Kitty and the man, at some point, he would have noticed the blood trail on the floor, either that night at closing, or in the morning, whenever he straightened things out and put all the chairs onto the tables. And neither Matt nor Festus sees any blood on the saloon floor.
As Matt and Festus come through the storeroom at the Long Branch, they come toward the camera and a curtain that they pass through to get to the door to the bar area. A shadow moves across the curtain, but there is no one there.
Apparently Kitty keeps the outside door to her storeroom unlocked. At night, wounded Crowley comes into the Long Branch that way and asks Kitty for help. Then the next morning, Matt and Festus come in that way, following the trail of blood.