[S]So, I was playing my friend who has Phoenix as anchor, and by chance I killed one of his characters with snapback to get her in. Now, in Vanilla, this would get the character you snapped in but when I did it here the second character came in instead.[/S]
[S]This isn’t completely game changing, but for the circumstance that I wanted (Phoenix coming in) this really sucks, since I waste a bar.[/S]
I figured people would want to know or something, since this doesn’t exactly happen often.
Hate to sound really lame/captain obvious, but you are 100% sure you used the correct button? Y’know, with the health bar positions changing and whatnot, I could see how someone could do that. Anyway, I’ve never seen that scenario happen, but some really weird stuff happens in Ultimate when you use commands to forcefully switch the characters. I know I was surprised when I realized that if you use assist # 1 in a combo and TAC, you automatically TAC to anchor. That’s what always happens to me, anyway.
I seriously wonder if stuff like this is a glitch, or if it’s just Capcom not telling us everything they changed. Then again, they probably changed the ability to decide who you snap in because Seth Killian found some hidden tech, and they decided to kill it before it was discovered. 
I feel bad for that guy some times having to be the official spoke person for Capcom’s bullshit. I mean for that to be the reasoning of a character nerf is just baffling when they buff Zero, but whatevs.
As for the OP I’m willing to bet you were confused by the HUD (no disrespect intended just a hunch).
A wild HUD appears
I’m assuming it’s mainly the fact that snapback hit frames are active on like the second frame; you can punish a Shinkuu Hadouken using Felicia’s snapback on reaction, for instance.
…if you excessively play Arcade Mode on Very Hard, you’ll notice how the CPUs actually use snapback as a makeshift Bionic Lancer, lol.****
Ok, it’s a false alarm, it still corresponds to who you snap in. I feel really stupid for not trying to test this, but I forgot that this particular player I was against would raw tag and mess up his order.
Again, sorry for bringing up something completely false. 
Actually this is not true. If your combo is long enough and gives enough time for the “assist” to reset, you can still get assist 1 in the TAC. For example I use Zero and Frank West and TAC frequently to level him up. I usually use Frank to extend the combo, make it lengthy, then TAC right into Frank. Give it a shot it works.
Honestly though the way TACs work with DHCs and whatnot is what I feel kills any purpose of “limiting” someone to using an assist once per combo because they really aren’t limiting anything. I used you as an assist? Ok i’ll make a long combo then THC or just DHC into you despite you being in the combo already. Meh random rant.
Yeah, I forgot to mention that. Still, it’s a change from Vanilla that wasn’t documented. I think Capcom really should have released a complete list of all the system changes, not just the major ones like side TAC. I noticed this when I was originally messing around with Wesker/Doom/Phoenix. I would use Doom beam to relaunch, and it would give me Phoenix when I TAC’d. A (former) Phoenix player’s worst nightmare. :o That is, aside from dat front page tech.