Been a bug for a while now I've tried with adobe chat support they pointed me here. Its not a consistent issue seems to happen to odd files here and there. Voted for the ticket but don't think they will fix it any time soon. FYI you can also replace the symbol in the top bar or add sometimes adding a coloured shape to the symbol then editing it at the end works as well

I have replicated this bug on a colleague's PC: the same happens on Windows 10 (same version of Illustrator 25.3.1).

The only workaround for now is to rename the duplicates in the Symbols panel (but not by adding a space and a number).

Here's an example again, copy-pasting from one file to another.

It pastes the wrong symbol (red instead of white), and there's no way to reload the original white one from the library to replace it with the correct one.

I have temporarily hidden the outline so you can see better what's happening.

Sorry again for the bad quality, I can't upload anything heavier than 20Mb.

I have to say, this is getting really annoying to have to work around this bug several times a day.

Not only does it impede workflow greatly, but it's a source of many errors if you're not paying attention to every little detail, simply when copy-pasting from a file to another!!

Newest update issue: When you copy and paste a symbol it will automatically replace itself with some other random symbol in your file. When you copy multiple (let's say 4) symbols from one document to another (I've also tried a brand new document) you'll end up with only 2 symbols in your symbols panel and 2 of them have been replaced with one of the other.

Illustrator 25.3.1 on MacOS Big Sur 11.4

Let's say I have 3 symbols, A, B and C.

A is the original symbol in my external Symbol Library file (blue in the attached video)
B is that symbol, imported into my current file and modified (I changed it to green in the video)
C is a duplicate of B, in my current file, also modified (red in the video)

When I copy C, I expect C to be pasted. But it's actually B.
(in the video, red is copied but green is pasted)

Moreover, when I try to "reimport" the original A (blue) by clicking on it in my Symbol Library panel, it thinks it's already in the file, when in fact it's B. Or when I drag and drop it, it imports B onto the Artboard.
Which means that when I modify symbols (which I do all the time), I can't access the original anymore.
Is it a conflict because they have the same name? And no I don't want to rename my Bs and Cs everytime I modify a Symbol.
It used to work just fine as you expect it to in Illustrator 22. It's pretty annoying. ;-)