Boggle Rules - Two same letters to make a word
I can find nothing in the official rules, nor in the Wikipedia article, that disallows using the same letter on different cubes. In fact, the Wikipedia article names some of the longest possible Boggle words and they include multiples of the same letter which would be impossible if that were the case.

It is definitely true that you cannot use the same cube more than once in a given word, nor can you spell the same word twice using different cubes. Where did you learn this rule - is it an official online implementation, or from someone telling you the rules, or elsewhere? It's likely that someone misinterpreted the rules, or was playing some kind of variant or house rule.