Honestly there were a ton of things, unless the weapons are made with magic.

BOTH Gunblades, Squall's and Lightning's. A sword cannot be combined with a real gun. That's an impossible weapon. And how did it not break whenever she blocked Odin's gigantic Zanteksuken?

But all of this could be said of the majority of the weapons in the later games.

The ages of SOME of the characters is really unrealistic. How is Eiko so competent and independent even though she's 6? Maybe she's a child prodigy? But even that wouldn't explain her emotional maturity? Even if a kid is working for NASA at age 12 (which HAS happened), they just can't deal with death like that at age 6. It's not possible.

As for how Cloud survived that fall? They're superhuman, you know. Same goes for why Squall survived Edea's Ice Strike, that and healing powers. Most of this can be explained when you take into account that they're superhuman.