The background characteristic options for faction agent seem to be the ones for the Acolyte instead in the character builder.

Using Chrome on desktop.

Regards

That is how the background Faction Agent is designed.

So they are.  According to the SCAG:

Use the tables for the acolyte background in the Player’s Handbook as the basis for your traits and motivations, modifying the entries when appropriate to suit your identity as a faction agent. (For instance, consider the words “faith” and “faction” to be interchangeable.)

So why not just do the replacement, or make a note in the section that suggests the above, rather than having it just appear wrong in the builder?

I see that piece you cited in the background description.

Also, the suggested replacements are suggestions, not the rule, so it is up to you to modify the words as you see fit.

Hi! 

I am not sure if this is the place to post this but the House Lyrandar Background doesn’t add proficiency with vehicles (sea/air). My educated guess is that there is no such “object” but perhaps if a new “object” called “Vehicles (air)” is created and the background aims to both and adds them it should solve it. Excuse me for “Stepping on your shoes” so to speak but wanted to help. 

There is one exception why the Acolyte is not totally perfect to be selected. Acolyte automagically gives you Religion proficiency, however, 5e lets the player to choose:

Skill Proficiencies: Insight and one Intelligence, Wisdom, or Charisma skill of your choice, as appropriate to your faction

Since currently it restricts the character generator to Religion being automagically selected, it's not a perfect choice for Faction Agents who not neccessary need or gets Religion proficiency from their faction.