It is open to interpretation and speculation regarding the exact nature of the closest thing to an encounter between Chigurh (Javier Bardem) and Bell (Tommy Lee Jones) in the movie. There are at least four possibilities.
1) Chigurh is indeed behind the door when we (and Bell) see what looks like his reflection through the lock tube. Bell draws his weapon and some time passes as he prepares himself to enter under the assumption that Chigurh is still inside. This may have given Chigurh some time to hide somewhere in the motel room. When Bell does enter, Chigurh is no longer behind the door (Bell doesn't even check there, although he does push the door open enough that if Chigurh were there he would probably know it). Bell checks the bathroom and finds the rear window locked. He then returns to the main room and sits down on the bed. He soon sees that the vent has been removed, implying that the money is gone and that Chigurh has it. During the time that Bell was in the bathroom it is possible that Chigurh left the room and escaped. Since Chigurh has the money he has no reason to go out of his way to kill Bell, and it is possible that he simply did the practical thing and escaped to avoid any further complications.
2) The second and third possibilities are similar but still distinct. They would be (2) that Chigurh is either in an adjacent room (the one to the left as we face the rooms as Bell walks towards them, for example) when we see him hiding behind the door (in what would have to be a mirrored shot due to the arrangement of the rooms) or
3) We see him hiding behind the door earlier in time by several minutes, being cautious about exiting the room. The first would make sense considering Moss' earlier method of hiding the money and making it accessible from another room. Other evidence to suggest this is the fact that both the room Moss was killed in (room 114) and the adjacent room (room 112) are behind police tape, implying both were part of the crime scene. It is difficult to determine by the film whether the lock was punched out in the adjacent room, however. The second would fit with the usual situation of Bell arriving moments too late to find Chigurh, which is one of the reasons he says that he might call him a "ghost." The fourth possibility is that Chigurh is already long gone and the reflection in the lock tube and the image of Chigurh waiting behind the door are all in Bell's imagination as expressions of his fear, the fear that he confronts (or attempts to confront) by entering the room anyway. There is strong evidence against any theory that Chigurh was not there when Sheriff Bell arrived. That evidence is the crime scene tape, the shadow of which can be seen on the door just as Sheriff Bell enters the room, projected by the headlights of Bell's car. This crime scene tape shadow is also projected on the wall of the hotel room after Bell opens the door. After Bell leaves the bathroom, he sits on the bed and we can see that the shadow of the crime scene tape is no longer on the wall, implying that it has been broken by someone escaping the hotel room, or the adjacent hotel room. However, it should be noted that the two pieces of crime scene tape are actually still intact when Bell sits on the bed, in other camera angles. While the tape shadow no longer appears on the large wall nearest the bathroom, the tape shadow still appears intact on the wall with the TV, when the camera is on Bell's face as he notices the ventilation grate has been removed. Just before the camera cuts away from Bell's face and to the ventilation grate, the two pieces of crime scene tape can briefly be seen flapping in the wind, showing they are still intact. Therefore, it is difficult to make any strong conclusions regarding a theory of someone (Chigurh) leaving and breaking the tape. It may be nothing more than an oversight in the scene's continuity.
Because we know that Chigurh was indeed there at some point, we could consider a combination of either possibility 2 or 3 combined with 4 as being what actually happened or what we are being shown. This would mean that we aren't seeing something that is purely Bell's imagination (although what we see may have been influenced by it), but instead what actually happened "5 minutes ago" or "in the next room over" might be shown to illustrate what Bell is feeling: that Chigurh is somewhere around and that he will be in danger upon entering the room. In other words, there was some trick editing where we are being shown a different time or a different place interlaced with the current time and/or location in such a way that makes it appear to be happening concurrently to the scenes with Bell. Other movies use this technique to fool the audience into thinking two things are happening in the movie at the same time in the same place, when in reality one has already happened or happened in a different place, or both.
In the end, it matters little where Chigurh was (which is one of the reasons it was left ambiguous). What is important is that we are shown that Bell thinks he is still in there and enters the room anyway, confronting his fear and possibly putting his soul at hazard. Once again he is too late and Chigurh is gone with the money, but he didn't know that before he entered the room. This matches closely the description of the scene from the book. The scene has been changed but the end result is basically the same. In the book it is clearly stated to the reader that Chigurh is still at the motel when Bell arrives. Chigurh is in the parking lot, notices a car coming and hides in his car as he watches Bell park and go inside the motel room. After Bell has finished searching the motel room he prepares to exit the room, and we "hear" what he is thinking. Just as he is about to exit the room he indicates that he is aware that Chigurh could be in one of the many cars in the parking lot, and that he would be helpless if Chigurh were to open fire on him from that vantage point. He exits the room anyway, gets in his car and drives down the road where he stops and watches the parking lot. He has called for backup and he waits until backup arrives, and when they do, a search of the parking lot returns nothing. The reader doesn't know how Chigurh escapes.