Our traffic numbers come from the same system we use to track our own website traffic, so we work very hard to make sure it is as accurate as possible, since we sell our own advertising based on those numbers, and if they were over-inflated, our other advertisers would complain vociferously.
I suspect the error lies in the affiliate program, who has an incentive to under-report.
However, if you'd like to provide us with the numbers you got from your affiliate program, we would be love to take a look and try to figure out what happened.
Edit: I forgot to mention that AdBlock blocks a lot of affiliate trackers, but a lot of reddit users specifically disable adblock for reddit, so that might also be a source of the discrepancy.