2. and 3. have the fewest mistakes. They still have two mistakes - there should be no comma after "three", and "graph" on the last line needs an article or other determiner. "can be total precise graph" also sounds strange. If you've copied it right, this exercise was probably not produced by a native speaker. You're right about the use of the semi-colon, but in 2, the clause which starts "no more than two of which" is not independent. The first clause is needed to identify the subject of the second one. "which" is a relative pronoun which replaces "them". The alternative is to start a new independent clause after a semi-colon or full stop / period, as in 3, and use "them", not "which".

I think you may have more issues here than the semi-colon, and in fact, I'm not really sure what you are trying to say. Perhaps I don't have enough familiarity with the background here, but I'm not sure what you mean with (a) "nodes" as compared to "intersections" and whether perhaps "intersections" means "intersecting curves" rather than the points where they intersect, and (b) "can be total precise graph", which is grammatically incorrect as it stands and needs to be resolved as either "can be totally precisely graphed" or "can be a totally precise graph". There is an apparently extraneous comma after "three". You also need to watch out for ambiguity in the antecedent when using pronouns like "them" and "which"; in the absence of clear context, the antecedent becomes the most recent available option, which is "each time" here, and probably not what you meant. One possible interpretation of what you are aiming for is: "These curves cross each other forming a line of nodes in each of which three of the curves intersect, of which at most two can be precisely graphed". But that's just my guess, and maybe it should be something else entirely!