OTA= Online Travel Agency

When you purchase a ticket through them they are not always buying it as a single ticket from the airline. They often purchase it at as a group of inventory at a "specialty" price. This prevents the airline from knowing how much you paid for the ticket. Since they do not know, they use the mileage to calculate the MQD to give you, like flying on a partner.

Here is United's verbiage

Certain specialty tickets (including but not limited to unpublished, consolidator/bulk, group, tour and opaque tickets where the fare you paid is not provided to United) will earn award miles based on the flight distance and the purchased fare class using the chart below:

Delta's

Certain types of tickets purchased through an agent, third party or part of a package, where the airfare price is frequently not shown when purchasing the ticket, are known as exception fares. Exception fares earn miles in a different way.