I suspect the first is due to the wording used by the Sword Coast Adventure guide; it's a choice determined by you and your DM. Which means it could be any language that you or your DM have determined, and not necessarily from the list of official languages. Not sure that the character wizard can handle that kind of thing.

As to other language choices I don't think that the CW looks at what languages you already have at any given point in the process so it's quite possible that you can get the same one twice from different areas and also it won't prompt for a choice in the case of the Clan Crafter since it won't know that you already have dwarvish and I'm pretty sure that the CW isn't coded in such a way as to check that and offer an alternative.

So these are all things that you'd clean up in the character sheet once the character is created.

The heading of the effect for Magic Resistance will need to be addressed in the ruleset since it's not a CW specific issue.