The easiest example to think about is both the fact that Sephiroth is controlling Jenova with his mind and thus the "Sephiroth" you keep following is actually just Jenova. It seems somewhat obvious but the game never clearly states that's what's really going on. The fact the forum still gets fans who needs this explained to them is evidence it was not properly explained.
The other is the deal with the Sephiroth clones. The term clones is somewhat misleading, giving the impression from the dialogue that Cloud was made in a test tube (which is only half true) and the game really gives no thorough translation for what the Reunion/Clone experiment really is. The PSX version's explanation is rather vague and can be interpreted in many ways from its actual meaning. I don't think I caught the fact that the Sephiroth "clones" featured in the game were actually the survivors of the Nibelheim incident until a few years later cause I believe Hojo only mentioned it once.
It also made Clouds origins a bit fuzzy cause technically making a SOLDIER and "Sephy Clone" is the same process except for mental instability. This explanation is given to you in several paragraphs in the game; whereas I just explained it in a single sentence. If you play through the original PSX versions, their explanation is overly convulated and requires a few read throughs to understand what's really going on.
The PSX version has a pretty bad translation/localization. I hear the PC version released later cleared all this up though.