[The following is all pure speculation based on (perhaps) a dubious source, so place whatever importance on it you may choose.]
Bodily fluids can be detected using various methods. We know for example that investigators used Luminol to look for blood evidence because of news articles. We know a Wood's lamp was used on JonBenet's body to look for semen during the autopsy. Since more things than just semen show up under UV light, what investigators thought might be semen was tested and found to be blood (JonBenet's) on her legs. I don't know all of the chemicals are that are used to look for bodily fluids, but I'm sure there is more than just Luminol. The following photo was leaked and printed in one of the tabloids. It shows a red area on the carpet outside of the WC. They (I think) misidentified it as blood. I believe it was actually a chemical sprayed on the carpet by CSIs looking for bodily fluids. It could possibly be the area where urine was detected. Once identified, the carpet area was removed and tested for positive identification in the forensics lab.
These are the reasons I suspect the red area in the following photo is where her bladder emptied into her clothes and into the carpet. Each of us can make up our own minds as to whether this might be what it is.
BTW, this area is approximately where the paint tray
had been when it was found. The two sets of golf clubs and other items had been moved around while CSIs were doing their testing, as shown in the following earlier photo: