I'm with Minato on this. Unlike Red XIII, Shin-Ra has no reason to capture a random, ordinary-looking woman who looks nothing like the Cetra sample they think they already have sitting in storage.
And there'd be no reason to go the complex fetus-injection route of creating a new one using cell samples from the frozen tentacly, winged thing when they have a talking, walking warm sample who just needs a little bump and grind to provide them with more of her kind.
Where was it stated she met Gast separately? I always thought he took her with him. Though I never took it as "helped her escape" he was in charge of Cetra research and so he took the subject with him then went AWOL.
How would Hojo know to come for her if they had just met after he left? What did Crisis Core "fuck up" here?
Well, Hojo says he had to search for them, though he implies that he'd known where they were for quite some time, and just waited for nature to take its course so that he could get both Ifalna and a hybrid:
Gast
Who could that--I was just about to...
Damn!!
How dare they intrude on our 'private time' together!
Ifalna
I'll send them away.
Yes, at once!!
Who the devil?
She goes to the door and opens it.
It, it's them!!
Hojo
Heh, heh, heh...... I've been searching for you, Ifalna... or should I say, Cetra!
Long time no see, Professor Gast!
Gast
Hojo... How did you know?
Hojo
Believe me, I had to turn over a stone or two to find you.
Two years I waited... That's how much I wanted this new sample...... Ha, ha, ha.
This bit doesn't make it terribly clear whether Hojo and Ifalna had met prior to this, though he does know her name and she knows it's "them," so eluding Shin-Ra doesn't seem altogether new to her either.
That being said, as we went over above, it makes no sense for them to have bothered with JENOVA if they already had Ifalna.
Also, the Ultimania Omega mentions that Ifalna was a local of Icicle Inn. On pg. 210, it says that Gast left Shin-Ra and moved his research to Icicle Inn. This is the next line after: 本当の古代種の生き残りである地元の女性イファルナと知り合い、聞き取り調査を開始した彼は、古代種の歴史をはじめジェノバの擬態能力やウェポン（→P.215）など、神羅も知らない事実いたどり着く。
"He begins to interview Ifalna -- an acquaintance and local woman who was a survivor of the true Ancients -- learning of JENOVA's mimicry ability and the WEAPONs, among other details in the history of the Ancients that were also unknown to Shin-Ra."
Granted, there's wiggle room there since it doesn't seem to explicitly say that Gast met her at Icicle Inn, rather than at Shin-Ra, but I'd say it seems implied. For that matter, if she were a local of Icicle Inn, were kidnapped there, and then escaped from Shin-Ra, it would be rather stupid to go right back where she was kidnapped from and expect to avoid recapture.
Of course, Crisis Core did outright retcon the bit of the UO where it says Aerith met Zack while selling flowers, so who knows if it even matters what the UO had to say on Ifalna and Gast's meeting place. At this point, the Compilation has all but removed Gast from ever even touching the JENOVA Project.
