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 overflow tube drains directly into the bowl, not the tank. The only way I can think that it would prevent the tank from filling is if it was cracked or had a hole in it and allowed tank water to drain into the bowl. If this was the case, you would notice the fill valve cycling if it was a slow leak or never shutting off if it were a large leak. The reason the tank fills quickly when you divert the bowl refill tube into the tank is that you are simply not splitting the water from the fill value between the tank and bowl any more.
It sounds like your fill valve assembly is the problem. The fill value has 2 outlets, one that directs into the tank, and the other that sends water into your bowl refill tube. My best guess is that something inside of the fill value got clogged with sediment, hard water deposits, or something else that restricted it. These are relatively cheap to replace and likely not worth the time to clean them out in my opinion.
Best Answer
The bump is most likely not necessary for a good seal.
Bumps like that are usually location devices for assembly (at the factory or on site). There's probably a corresponding dimple or slot on the hard parts of the toilet. They allow for quicker and more accurate manufacturing.
So just be sure that your new seal stays in the correct position as you tighten things up.