So, doing some research for this question I found an anomaly in the Moveset Searcher, it displays Egg Moves that are incompatible with each other. Deciding to investigate further, I discovered this phenomenon everywhere!
For example: The Calculator says Gigalith can learn both Heavy Slam and Lock-On, despite it clearly needing two different fathers to achieve this. The same goes for Spiritomb with Nightmare and SmokeScreen. It is not just for these Pokemons, the problem is almost everywhere.
I also tried to give these Pokémon their respective Egg Moves on Showdown, and it said they could not learn both.
Is this just a massive glitch or is the Calculator not advanced enough to separate the Egg Moves. Or can Egg Moves be passed down through the mother in some way?
I realize this isn`t a huge or urgent problem, but it migth cause a bit of confusion and i just wanted to highlight the issue.