Question about yellow in toilet bowl?

Yes, it's related. There is a slow blockage which prevents a complete water change. So, some of the bacteria-ridden water remains, enough to discolor it. Pour half a cup of bleach into the toilet bowl. Swish it around carefully, up under the rim, and let it sit for an hour. Then flush. See if that fixes it. Repeat if necessary.

You will have to play detective and figure out the source of the color. The first thing I would do is empty the commode and turn off the water. Then go get a bucket of water from another source where you know the water does not cause the problem and fill the commode with the different water. Wait til next day and see if the problem occurs. That should tell you if the problem is the commode or the water.

More than likely you have hard water in your area. Your statement that you have to flush twice may be an indication that the water ports on the underside of your toilet bowl may be clogged with calcium deposits. Clean all of them out with a small flat blade screwdriver or anything else you can use to remove the deposits. Also check the flapper to see if it is coming up far enough to allow for proper flushing. Replace the flapper if it is covered in deposits. Another thing that can cause this is someone urinating in the toilet and not flushing it. The urine standing all night will cause stains.

Could be copper from the cistern.