This is going to be long and technical, but here goes...

Block codeshares where each marketing carrier has a fixed block of seats on the operating carrier flight are pretty rare in modern times. The only carrier I know of that uses them frequently still is QF (mainly on their CZ / CI codeshare flights). From the operating carrier point of view, you don't want to cede that level of pricing control to the marketing carrier. In a block codeshare arrangement the marketing carrier's revenue management team manages their inventory as if it was their own flight so could choose to sell theirentire block in the cheapest class while the operating carrier is holding out for high fares.

Instead most codeshares today are freesale, which means the marketing carrier can sell as many seats as they can (or sometimes with a max), but the inventory allocation always comes from the operating carrier.

The most common reasons for discrepancies in codeshare pricing are:
1) Inventory is generally not real time. The marketing carrier receives the inventory allocation from the operating carrier in an AVS message through the GDS. This can cause discrepancies when the operating carrier sells a decent number of seats thus closing inventory buckets, but doesn't trigger a new AVS message to the marketing carriers with the new inventory allocation. In this scenario, sometimes the marketing carrier is able to sell the lower (and outdated) inventory allocation, but sometimes when you go to sell, you'll get a message back that that bucket is no longer available. The operating carrier may set a rule that says, for example, in discount buckets only send 80% of the seats available to the marketing carrier, but that would result in a scenario where the operating carrier is cheaper than the marketing carrier, which isn't the case here.

2) Inventory bucket mapping. If the operating carrier uses 10 buckets in economy, but the marketing carrier uses more or less, two buckets on one carrier can map to one bucket on the other carrier. If not done correctly, it can cause the marketing or operating carrier to fall out of sync price-wise. Assume the operating carrier only has buckets Y and B, but the marketing carrier has Y, B, and H. The codeshare agreement could say that H on the marketing carrier is B on the operating carrier and that Y and B on the marketing carrier are Y on the operating carrier. If the operating carrier closes B, then H closes on the marketing carrier. The operating carrier is now selling Y, but the marketing carrier is selling B. Assuming they both have the same Y price, the marketing carrier must now be selling a lower fare.

3) Fare structure differences. The marketing and operating carriers set their own fares in the market (and outside of a JV) cannot talk about those prices. So the marketing and operating carriers may have different fares for the same bucket or the conditions may differ (advance purchase, min/max stays, etc.). In this case, they are both selling the same bucket, but their fares are different in some way so one is more expensive than the other.

Hope this helps someone out there...