Learn English – either because or because

I think the best way is:

Indeed, the absence of a segment causes a lack of graph edges which refer to that segment, leading to a distorted cycle which produces a fault corner.

Alternatively:

Indeed, the absence of a segment causes a lack of graph edges referring to that segment, leading to a distorted cycle that produces a fault corner.

This assumes that the prior sentences cause the "indeed" to make sense. Otherwise, remove it.

Your statement looks fine to me, although I have corrected a few unrelated grammatical errors because it helps to make the question clearer. :)

Although in this case is suggesting that an exception to a rule has been made. Here, the implied rule is that a graph representation is expected to be a complete one. It's perfectly reasonable to use because in the clause that explains why the exception has been made. Here's another example, using the recent Kentucky Derby result:

Although California Chrome won without a particularly fast time, this was because Espinoza eased him up at the end to save him for the Preakness.

The "rule" is that you want to run at a time comparable to the other great horses. The exception is that he was running fast enough to win and had another race to run soon.