LOL! That happens!
When I first started, I was working on creating my own breeding charts and not worrying about finding the Magic Plants. I started two different games and just started documenting the crosses as they came, as well as keeping track of which combinations
either game found.
Four of the Magic Plants happened without explicitly aiming for any (except the easiest one to find...) If I found a MP in one game, then I would note it in my "all species" chart, knowing that I would come back to it later.
I also worked on my all-species charts as well, and if I didn't have a new cross to make, I would see if crossing a mature plant with any other I had in the greenhouse would make something new. If it was a new MP (for that game) that was a bonus!
In a game at work I started playing with the Mutation Liquid and created my Pocket Guide. During that process I discovered the fifth plant.
Back home, as I continued filling in my all-species chart, I would keep track of what seeds showed up in the store. When I saw an interesting Tier 3/Tier 3 seed I bought it and was excited when the seed was planted because it had a higher than usual price! And yes, when that plant matured it was the sixth Magic Plant!
I still didn't have all six in any one game, but now I knew what they all were.
Eventually, through breeding, mutation, new seeds, mutation, and breeding*, I got all six in my main two home games. (So of course I started a third!)
So hang in there, eventually you'll be able to breed to find them all.
If you don't know what the flowers/foliage for each of the plants are, you may want to work on several different games at once like I did and then combine the data.
If you do know, then keep an eye on the store for the right seed to appear and take the chance. Even if it is not the right seed, it may help with another plant you already have for a cross-breed, or won't be too many mutation hits away to your goal. (Read my Mutation guide before trying this, or you may end up spending too much for not a lot of progress.)
* I was really frustrated with one of the MPs in one of my home game. I couldn't seem to make the right plants to cross-breed. I finally found another seed/plant that was close in both the flower and foliage and mutated that. It didn't get what I wanted, but it did create a plant that I could cross with another I already had to make the MP.