I just ran a test using the "observe" command.

Apparently, the Xindis don't appear unless there are at least 60 AI empires on a large Milky Way map.

What do you mean about the Enterprise? Why are you expecting it to be present at game start unless you're playing the Borg Temporal Incursion?

That's strange, in all previous playthroughs I got it quite early, but this is the first time I've chosen the canonical option for the crisis.

Well there's an element of RNG. In some games you might not get the event, and in others you might not roll the ship before you progress beyond it.

Regarding the Xindi, I've played about twenty games.

With any nation other than Earth, they function normally.

With humans, the Azati system isn't created unless there are 60 or more empires in the settings.

With 50 empires, the Azati system is created, the planet is colonized by the Xindi, they have a fleet but no space station in the system.

As a result, the game removes the Xindi and even the system.

With any other empire, the Xindi have a space station and the faction remains in the game.

Is this normal or a bug?

It's by design - we can't really handle the Expanse event chain properly if you can encounter the on-map Xindi too early.