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I've been attempting the Pomeg Berry Glitch in Pokemon Emerald for a while now and I feel like I'm doing something wrong;

I caught a fresh Makuhita from VIctory Road(no EVs), taught it Rock Smash as it's first move(which would produce a Lugia due to the number of the move), and cloned it many times using the Battle Frontier cloning glitch.

I placed them in Box 1 and 2(labeled Pomeg 1 and 2 respectivally) in a lined pattern, each line next to a line of cloned versions of the in-game trade Plusle PLUSES with no EVs and the only move being Growl(I did this as a corruption initiator).

I performed the glitch lots of times but I whenever I get a Makuhita to turn into a regular egg, it hatches into another Makuhita instead of a Lugia.

I was using a Breloom as the Pokemon I used the Pomeg Berry on, a Rayquaza as a fainted flyer(in case the map data gets corrupted) and a Gardevoir as the Pokemon I switch into battle right before I use the berry then put in my PC.

In case it matters, whenever PLUSES turnes into a regular egg, it hatches into a Vileplume.

I've gone on every site and watched every video on it(mainly Werster's) but I still can't find an answer.

Am I doing something wrong or am I just getting super unlucky?? Please answer I need this glitch to work for my Livingdex.

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Have you seen this video? It gives the best explanation I've seen on how to get started with Glitzer Popping. I have a bit of experience with this glitch, so I'll also give my own rundown.

It sounds like you just caught a random Makuhita off of Victory Road. If that's the case, then there's your problem. In order for the glitch to work properly, you need to know the Pokémon's PID value, which for any Pokémon other than ingame trades, can only really be found by using an RNG Reporter. This video goes over why the PID is important and how to use the RNG Reporter to obtain desirable PIDs. However, this is only really useful for more advanced Glitzer Popping, and is unnecessary if all you want is a specific Pokémon like a legendary. For simplicity, I would recommend just using the ingame trade Pokémon Pluses the Plusle and Dots the Seedot (or Nuzleaf/Shiftry; it doesn't matter if it's evolved).

Here's a simple list of what you need to do:

  • Delete all of Pluses' moves except for Growl.
  • Teach Dots the move Flash in its fourth move slot (in English version). The other three slots don't matter.
  • You will need to EV train Dots' HP and Atk to match the species ID of the Pokémon you want. The EVs you need vary depending on the Pokémon you want, so I made this tool to help out.
  • Clone Pluses and Dots at least 7 times each and line them up in an alternating pattern, starting with Pluses.
  • Perform the corruption. I would recommend using a Ghost-type with Curse and odd HP as the Pokémon that you use the Pomeg Berry on, since it can quickly get itself down to 1 HP, but it's not necessary.
  • When one of your Dots turns into a regular egg, put that egg into the last slot of your party and enter a battle with it without healing your party. In the battle, you'll be able to see the Pokémon inside. If it's still Seedot/Nuzleaf/Shiftry, reset and retry. If it's your target, hatch the egg and save. If it's anything else, you messed up somewhere during setup and need to start from scratch.

Dots' fourth move in other languages are as follows: none for French; Hidden Power for Spanish; Nature Power for Italian; Rock Smash for Japanese.
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I had though of using SEASOR, the in-game trade Horsea to hatch the Pokemon I needed in Pokedex order(starting from Articuno to Jirachi) but then I saw that other Werster method and tried it. I think I'll go back to my original plan(what you said to do) but with DOTS like you said. Thanks for the answer it was driving me crazy.
My Main Goal with this is to get Lugia with PokéRus. So i trained Dots to have 249 HP EV's and did all the other steps. And also the Glitch seems to work fine, with the exception that i only get bad eggs instead of regular eggs. Also my Dots knows Flash in the fourth slot in my German version. My Question now is, whats the fourth move in the German version supposed to be, and how big is the impact of miscountingt on the EV training, will it just be another Pokémon with Pokerus or will completly screw me up?
The video doesn’t specify what move you should have for the German version, unfortunately. However, I could be wrong on this, but the video description does seem to suggest that the fourth slot is only important if you’re doing double corruption, which your case shouldn’t need. It’s possible that you’re just getting unlucky, since a bit of RNG is involved with the corruption.
As for the EVs, having the wrong EVs could have varying results, I’m honestly not sure. If your HP EVs are slightly off, then as long as you have less than 252 EVs, you shouldn’t have any problems; you’ll just get a Pokémon other than Lugia. If your Atk EVs are off, then you could get some weird results, since you’ll end up with a glitch Pokémon. I wouldn’t imagine that this would have much of an effect on the corruption itself, though, and realistically, the worst a glitch Pokémon might do to your game is freeze it, in which case just turn it off and it should be fine.