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.

The flange should sit on top of the finished floor, if it doesn't you'll have to modify the plumbing or find another way to achieve this.

Notice in this image how the toilet waste pipe sits just inside the flange opening, this is the proper way for a toilet to sit on a flange. Even without a wax ring, this union is not likely to leak under normal circumstances (I'm not recommending a wax ring not be used).

Wax as a waste pipe?

Some folks recommend using a thicker wax ring, or even doubling up wax rings. The problem with this, is that you end up with a waste pipe made from wax. Now this might hold up, but more than likely it's eventually going to fail, and leak.

Modify the plumbing

If you have access to the flange from below, you might be able to modify the plumbing to make the flange sit atop the floor. In most cases, however, this is not an option.

Adapters

There are adapters available, that solve this exact problem. The Set-Rite Toilet Flange Extender Kit; described in the answers to this question, Comes with different size spacers, which allows it to compensate for various sized offsets.