
Origin Feat
You gain the following benefits.
Two Cantrips. You learn two cantrips of your choice from the Wizard spell list. Intelligence, Wisdom, or Charisma is your spellcasting ability for this feat’s spells (choose when you select this feat).
Level 1 Spell. Choose a level 1 spell from the same list you selected for this feat’s cantrips. You always have that spell prepared. You can cast it once without a spell slot, and you regain the ability to cast it in that way when you finish a Long Rest. You can also cast the spell using any spell slots you have.
Spell Change. Whenever you gain a new level, you can replace one of the spells you chose for this feat with a different spell of the same level from the chosen spell list.
Repeatable. You can take this feat more than once, but you must choose a different spell list each time.

On the D&D Beyond app, I have a Warlock character that took the Magic Initiate feat. The 1st level spell he has prepared is Witch Bolt. It shows as a spell that can be cast once per long rest without using a spell slot, but Witch Bolt does not show as an option that can be cast using a spell slot (I want to be able to use it as a 2nd or 3rd level spell). Is this a mistake / glitch? Or can I not use it with a spell slot?
I am curious if the spells from the feat would count as a spell from your native casting class. In your case, would Witch Bolt be a Warlock spell for the purposes of Pact Magic or is it solely a Wizard spell (using the spellcasting modifier when you chose this feat)?
I'm having the same issue with my cleric who has Find Familiar from this, only shows up as something I can use once per long rest. I also have false life from my level 3 chthonic tiefling species, that has the same type of text about always being prepared and and being able to be used once without spellslot per long rest, but that shows up three times, once with "use" (once per long rest) and once at each of my spell slots levels (1 and 2) as "cast"
So I don't think it has to do with the Warlock's Pact Magic (also, those are still spell slots, it doesn't say it's limited to spell slots from "Spellcasting Ability" (i.e. the class feature used to cast spells for every magic class except Warlock) or anything like that, so I'm pretty sure it's a glitch
I think it's a glitch, too. I have the same issue with Magic Initiate (Wizard); the 1st-level spell I chose shows up with a "Use" button, renewable by Long Rest, but not as a spell that I can cast using spell slots (and it's a spell that would benefit from being cast with higher-level slots).