Like I said... I would probably do an emergency water change. What has your cleaning schedule been like so far?
And to be perfectly honest with you... 3 gallons/12L is too small for anything but a betta fish, or shrimp. Not to mention your tank is kind of... really over-stocked.
Neon tetras should be in groups of at least 5, and they are very sensitive to ammonia/nitrates. They should be in at least a 10 gallon tank (around 38L). The same is true for the black neon tetra, and I think for the x-ray as well.
White Cloud Mountain Minnows are awesome and really hardy... but they do best in schools. You could probably get away with a five gallon/ 18L tank, but Id still reccommend at least the 10 gallon/38L.
Red Minors/ Serpae Tetra can be really nippy and need large schools to combat aggression. For the larger tetra, I usually suggest at least 20 gallons/ 75L. They *should* be in schools of 8 or more, but usually you can get away with 6 or so.
Kuhli loaches... again, they do best in groups or they tend to hide alot more. You could probably get away with two in a five gallon, but if you want a nice selection of fish with them, you would need a ten gallon or so.