Legendary Pokemon duplicates? (anime)?

Question

Something I always wonder is that...
Red has supposedly captured the three legendary birds: Articuno, Zapdos, and Zapdos. as we seen from Pokemon origin. He also went to capture Mew two later on.
Many people believe, (including me) that Red set out his journey before Ash and they are possibly related or know each other in someways. which means they are.... err.... in the same universe or time dimension. Then how come we still see Ash encounter with all these legendary Pokemon that are supposedly been caught already at an earlier time by Red?

Answer 1

Okay well, first of all, it's already known that the Anime and Game timelines take place in two different parallel universes (and the Adventures Manga also has its own universe, which of course gives the other, somewhat less popular and important, Pokemon Manga their own universes too.)

There are multiple legendary birds. There have been several legendary birds in the anime (and they've all been different individuals). They of course got featured in Pokemon Movie 2000, along with Lugia, who would later reappear as a baby Lugia (and of course, suggesting another Lugia which is possibly the same one from the movie. However, the movies aren't canon to the anime, so it's not likely)
Later in the Diamond and Pearl series Team Rocket saw a Zapdos fly by. But if I remember correctly, they could not pursue it because it shot down their balloon.

Articuno appeared in the Johto League Saga. I can't think of a non movie appearance of Moltres, but I'm pretty sure there has been one.

The Legendary Beasts have shown up a LOOOOT in the anime. In the chronicles, in the Pikachu shorts, in the Johto Saga, in the third movie, in the 13th movie (but they were illusions. however, I think the ones in the third movie were also illusions), etc...

Red is the Ash of the game world; Ash is the Red of the anime world.

The Origins also has its own universe. If, perhaps, there were another Red and Blue (oh and of course, Gary is the anime version of Blue)remake, it would probably be based on the Origins Special.

Ash has never met Red, and never will (unless the anime writers decide to go Super Ultra Weird Mode...although this would be possible considering how a few Pokemon can cross through dimensions).

You see, if they were in the same universe, this would not make sense. In the anime a guy named Dr Fuji created Mewtwo with Team Rocket. In the games, he was seemingly only made by TR (although Fuji appears as Mr. Fuji in the games, and this is even further hinted at in the Origins Special). Later of course, another Mewtwo was cloned in the anime.

Aaaannyway! Sorry if that was too long. But the fact is: the games and anime are in different universes, and there isn't a confirmed number of Legendary Pokemon that can exist in any universe. I believe that after the heros (players) of the games catch Legendary Pokemon that are very important to the universe, Arceus (if he was captured then.. I have no idea :O), or another important Pokemon creates a replacement for them.

Answer 2

We do not know if there legendary Pokemon duplicates because we don't know if Ash and Red are in the same universe. There are a few reasons why Red and Ash are most likely not in the same universe

-Pokemon Origins is Based of of Pokemon Red and Blue, the anime is not based off of the games.
-Both Red and Ash are from Pallet Town and they don't seem to know anything about each other.
-Team Rocket Grunts (as far as I know) are almost never seen in the amie, they are seen very often in Pokemon Origins.
-Near the end of Pokemon Origins, Red convinces Geovanni to become a "good guy" however, he is not the least bit friendly in the anime.
-The Pokemon League is much different. In Pokemon Origins the Pokemon League is based off of the league in the games, while in the anime it is totally different (as far as I know) from the video games.

There is one huge hint that Red and ash are not in the same universe. Pokemon Origins is based off of the games, in the games you can only catch legendary Pokemon once, unless you trade. In the anime, there could be as many legendary Pokemon of the same type as the anime people want, because it is not based off of the games. If Red and Ash were in the same universe, there shouldn't be more than one of the Legendary Birds and Mewtwo.

So as far as we know, there are not Legendary Bird and Mewtwo duplicates.
But, as I said above, we have no proof that Ash and Red are in the same universe, just theories.
(Note:
This is not an exact answer because we don't know the actual answer.
These are just my theories.
I may have some things about anime details (like the Rocket grunts not being in the anime) wrong because I have not watched much of the anime, but enough to make this theory)
Hope I helped!