By the way, it is not at all easy for this to be sewage getting into your water lines, but it might be a problem of siphoning back into your house lines from the toilet tank itself. If so, it is still a bad thing that really must be repaired. I like the idea of a couple of drops of food coloring as a test of this. It might happen only when the toilet is flushed, and the faucet for the sink is also open.
If that test shows nothing, then redo the test, but this time, turn off the water pressure into your home at the main supply. (There will be a shutoff valve in your basement.) Now, open the valves in your downstairs faucets. This will create a siphoning effect, trying to suck water back from the toilet supply tank.
Since this has happened only once, my guess is it happened when the water pressure for your home was turned off. This allowed water to siphon back into the water supply lines from the toilet tank. An old valve in the tank might explain that.
Regardless, if you confirm this is what happens, then I would add an anti-siphon valve (also known as a back-flow prevention valve) into the water line to the tank. This is a spring loaded one-way valve, that allows water to flow into the tank, but not the other way.
Could this be a copper corrosion issue as the plumber claimed? This seems unlikely for that to have happened since you have not seen it before, but anything is possible. If you have that much copper in your water that is leaching out of the supply lines, this would be something to worry about. So if you do the food coloring test, and there is no sign of backflow from the tank, then I would get a water test done for copper. In fact, a quick check on Amazon finds a home water test kit that includes a test for copper in your water.
It seems as if you have an obstruction that may be floating around in the pipe or valve. Sometimes it obstructs sometimes it flows clear. I would start with changing the water valve. If this is the old style "gate" valve there are several things that can clog the line. I would replace it with a 1/4 turn ball valve. That will give you much better flow than a gate valve. You will need to shut down the water probably at the main. The old valve is probably soldered, but you could cut it off and use a compression type valve instead. "Sharkbite" is one such supplier. Although I have never used their compression valve, I have used their end caps and found them to work well.
If you can have someone hold a bucket under the pipe once you cut off the valve and then a second person turns on the water main to fill the bucket to purge the line of any debris. With cast iron pipes it is common to get clogs from rust build up. The rust may not pass the small opening in the old gate valve when you first purged the line.. Although you did not mention what type of pipes you have, if it's copper than you won't normally find rust obstructions..
Best Answer
The caps come with a washer-type thing that they clip into:
Your toilet clearly does not have these clips. Using silicone is most definitely not the correct way to attach these, so maybe the installer lost the clips or just has never installed a toilet before?
It's normal to cut the bolts to length, as the length needed depends on the thickness of your floor. The nice way to do this is with a tool that has a cut-off wheel (eg, Dremel), the not-so-nice way is a pair of cutters since it leaves the edges sharp, but if the cap is attached correctly it shouldn't matter.
Here's what it looks like normally (via Handymanhowto), the clips are clear in this case: