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.
No filter removes all contaminants. Carbon is great for improving the taste. The white ones remove large sediment. Activated alumina removes some fluoride among other things. Distilled water will be free of most things but volatile chemicals will make it through. UV light and micropores (ceramic and "nano tubes") will remove most virus bacteria protozoa and cysts. Uv light will kill most if not all of those little nasties if the flow is right.
So the first step would be to go get your unfiltered water tested. Then see what's in it that concerns you then figure out what you need to remove those contaminants. Your filter might not be designed to remove the stuff you have a problem with.
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My Co-op's "plumbers" came this morning and they finally used a hand tool which they refer to as a "Blaster", they first used it on the hot/cold valve with the cartridge removed - the flow got a little better - then I asked them to use it on the tube spout copper pipe - after several attempts BINGO, FULL pressure water flow has returned. There was evidently "something" between the hot/cold valve & the tubs copper spout that needed a really strong push to get knocked out. All we saw was some brown water and a few very small pieces of rust. This is the 3rd time this has occurred this year, so I have become an unfortunate experienced person at what needs to be done. If I had a "blaster" I likely could have taken care of it and I might just get one.