There's a lot of confusion with the anti-matter stuff, but basically if you don't have the DLC ship you'll be given the element by some alien in your system. If you have the DLC ship, you're already fueled, so the game skips that part and immediately leads you to the next step, which is warping out of the system and on to the next.
Once arriving and scanning the next system, you'll find a beacon that leads you towards the anti-matter recipe, which is required to continue your adventure.
There's no way to continue with the game without the anti-matter recipe, therefore it's impossible to miss it. The DLC ship doesn't glitch anything, it just assumes the player is going to continue with the game and eventually run into the next part of the quest.
Some of the best advice I can give to anyone playing this game, is not to worry about trying to find the right way to do things, as the game will lead you towards the center of the universe. Scan when you're near a planet in space, and continue to scan while you're walking about the planet.
Find your own path. Don't be afraid to change up your way point, or explore the universe because you might miss something. You won't. If you're in the star map and see an interesting looking sun, start heading there and see what's up. The game has a narrative and you'll get all of that as you continue towards the center.