Before the battle with Trance Kuja, he says that even if Zidane wins Gaia will become Terra because of the Lifa tree... However, after the final battle when Zidane go see Kuja, the Lifa tree is getting crazy and then...
Some time latter...
Everything is normal... why?

Cuz the cycle of souls had been disrupted, so the tree couldn't serve its original purpose, so it went all crazy.

I know that, my question is why it as stopped? Gaia was supposed to become Terra... but for some reason it hasn't...

Well, Terra wasn't there anymore, thanks to Kuja.
Why the tree finally stopped doing what it did, well, it just lost its energy after a while of being all crazy, it's "just a plant", so, yeah...

The Destruction of the Crystal changed evrything

The Crystal wasn't actually destroyed - Kuja merely threatened it - which was enough to draw out Necron. Even threatening to destroy the Crystal is enough to summon Necron, as where the Crystal is the origin of existence, life, memory and creation, Necron destroys it - in an attempt to return the universe back into nothingness. (shades of FFV's storyline here).

Necron mistakenly believed that Kuja was actually acting on behalf of all creation - that life and the universe no longer wanted to exist, and so was more than willing to send everything back into formless, primeval chaos. Defeating Necron proved that life and order still wanted to exist, against what Kuja's misguided actions might have meant, and so Necron had no choice but to return to whatever dark void it was born in, awaiting a time where creation will cease to exist.

Accordingly, once Necron was destroyed and Kuja died, the Crystal also simply returned to wherever it was originally spatially located (hence, why it's shown in the very last moments after the end credits have completed).

The Crystal wasn't actually destroyed - Kuja merely threatened it - which was enough to draw out Necron. Even threatening to destroy the Crystal is enough to summon Necron, as where the Crystal is the origin of existence, life, memory and creation, Necron destroys it - in an attempt to return the universe back into nothingness. (shades of FFV's storyline here).

Necron mistakenly believed that Kuja was actually acting on behalf of all creation - that life and the universe no longer wanted to exist, and so was more than willing to send everything back into formless, primeval chaos. Defeating Necron proved that life and order still wanted to exist, against what Kuja's misguided actions might have meant, and so Necron had no choice but to return to whatever dark void it was born in, awaiting a time where creation will cease to exist.

Accordingly, once Necron was destroyed and Kuja died, the Crystal also simply returned to wherever it was originally spatially located (hence, why it's shown in the very last moments after the end credits have completed).
Yes but they dont show us how Zidane escapes and what hapend to Lifa Tree.Also what hapend to Kuja.....well probably died but if he did how Zidane escaped?

The obvious idea is that Zidane somehow managed to avoid being crushed by the roots of the Iifa Tree (being a Thief, he was extremely agile, so it's little wonder he could have jumped clear in the last split second. He was probably injured while escaping though, which explained why it took him so long to reunite with Garnet and the others.).

Most likely though, Mikoto probably helped him escape too, as she too was left behind when the Lindblum and Alexandrian Airforces departed (she's shown standing on a root looking up at the Tree, when Zidane is narrating in 'voice over' about Kuja).

Kuja on the other hand, almost definetely died, either when he collapsed in Zidane's arms or when the roots crashed down on them. No other explanation is needed for him really.

Incidentally, the Japanese FFIX Ultimania books apparently explain all of FFIX's plotlines and story, so I assume they would therefore finally explain how Zidane managed to survive and whether Kuja perished or not. But, as those books are unavailable outside the land of the rising sun (and are not avaialble in English either), they guard their secrets to all but those lucky enough to read Japanese fluently. Sigh...