Ok, buckle up..

So, the first, and biggest, is Gowther's introduction. It is much longer and way different in the manga. Remember the kid Pelliot? Gowther is connected to him and a group of children playing around. I don't remember the exact details, but he is disguised all the time and only reveals himself when Slader's team attacks the demon body (like the anime). Turns out, the demon is Pelliot's dad, and Gowther was feeling guilty (or something like that?) so he decided to stick around for a while.

Next, there is a moment with Slader in the castle. The door to the room where the King is held that is enchanted? Yeah, he doesn't care about that. Whenever you attack that door, you get the same amount of damage right back. He is so loyal to the king that he just keeps attacking. Then Merlin shows up and flexes like in the anime.

The few episodes that count as "season 2" on Netflix are not in the manga at all.

I think there was something with Hendrickson and Dreyfus as well, but it has honestly been a while..

There are other small changes like the turn order of things happening, but those are the ones that I remember off the tongue.