It's been a few years since I had played it, but this is the problem in more detail:

Any mission that has a cutscene- so most or all story missions- cannot be joined unless the host and joining players have all seen any cutscenes. Every person has to see the cutscene at the beginning of the hunt, so all new players have to load the hunt, find the monster, watch the cutscene after you found it, then all but one leaves their hunt and joins him. So you presumably launched an SOS flare for your friend after any cutscenes, or on your second attempt after watching them, and your friend had already played the mission, so he had already seen it. If you had both been new, you would have both had to play the mission alone until after any cutscenes, then one would invite the other. I had thought that the joiners would additionally not get credit for completion, but it seems like that's not true, but it's still a lot of additional friction with no real justification.