skibum - 7:45 am on Jan 16, 2013 (gmt 0)
It is generally not a deliberate thing when tracking tags are implemented incorrectly, at least in my experience. It wasn't just affiliate tracking tags but the tracking tags for search programs, tracking tags for email campaigns, tracking tags for media campaigns and most any other type of campaign.
The marketing agency would handle or consult on marketing and promotion. Sometimes there would be as many as 5 different agencies on one client. There were UI people, designers, and often IT departments who understood the programming, hosting and development who were waaaaaaaaaay overworked and had no insight into what tracking tags were, why they were important and often times lacked the instructions to properly implement them.
It wasn't specific to affiliate programs. Campaigns that the CEO or the CMO or some other executive would be watching with eagle eyes and wanting to micromanage would come back with zero sales or missing sales, clicks or other key metrics. In other words, tags would get screwed up for the most high profile campaigns a company ran where they were outlaying their own money up front and expecting to see results.
The problem was with implementing tracking tags in general and not specific to affiliate tracking tags. That is not to say there are no advertisers out there who may deliberately omit affiliate tracking tags but across lots of industries from homebuilders to retail to financial services and healthcare all kinds of tracking tags got screwed up.