Let’s call it a “passive oversight”, in that yes, I didn’t think of it, but also, the first 2/3 of the Clone Wars were a transitional period where both types of armour appeared side by side as the earlier was being phased out.
…Unless it’s named characters actually reverting their armour update on-screen, in which case, yeah, regular oversight.
Yeah, there’s a bit of snag in the Rako Hardeen ep. where you see Rex and some other 501st troops in their Phase II armor in Plap’s office. I suppose you could just shift the order on the list so Citadel places before that arc.