double negatives

If what is bothering you is the repetition, not the double negatives, then you could simply change it to:

There was no clause left in the sole agency contract that wasn't a source of conflict.

"There wasn't a single X left in..." is an expression with a specific effect, so if your author wants that, I would understand. Your version is certainly cleaner, but it does lack this effect.

I agree that it's much cleaner without the double negative.

Double negatives come up a lot in my field: the law. In California, for example, juries in criminal cases are instructed that "reasonable doubt" means something “that leaves the minds of the jurors in that condition that they cannot say that they feel an abiding conviction . . . of the truth of the charge.”

The law is not without other examples. (I slay myself.)

For those who'd like to read more, please see http://thepartyofthefirstpart.blogspot.com/2007/04/column-twelve-confused-men.html

Yes, you're being pedantic.
And repeating the word "wasn't" has nothing to do with it.

I realize this is an old question, but what neither the questioner nor any of the three previous answerers notice is that what is being discussed here is not the use of a double negative. A double negative is the use of two forms of negation in one clause, as in "I can't get no (satisfaction?). The sentence being discussed here uses two negatives, but in different clauses.

However, I agree with the questioner that it is an awkward sentence. It is not bad – or improper – English to repeat 'wasn't' in this case; the author is trying to use matching phrasal structures, which is a 'literary device'. What makes the sentence awkward is the intervening clause "in the sole agency contract," which interrupts the matched clauses.

I would have preferred: "In the sole agency contract, there wasn't a clause left that wasn't a source of conflict."

Double negatives are not prohibited. You may be thinking of instances where the actual meaning differs from the words (e.g. I don't have no money to mean I have no money).

Style dictatates it should be in the simple and positive form, as you suggested. Yet, if the author wishes it this way to make some point, it is not incorrect (notice double neg here).