Reasons I've been denied jobs in the past:
-- Overqualfied, afraid I was going to bolt when a better paying gig came along.
I've had that.
-- Worked for their competitor, how do they know I'm going a corporate spy. I left Regal and a bit over a year later applied for a part-time weekend usher job at a Carmike much closer to home.

-- Based on my resume, I might get their (the interviewer's) job. The supervisor giving the interview was on probation and was looking for a-- in her words-- "total fuck up" so that the company would keep her.
My wife missed out on a job because of that. The interviewer was a moron, to the point where a supervisor noticed how my wife was breezing right through it. The interviewer "lost her application" afterward.
-- Married to a immigrant, and they're a "American" company and don't support "Green card marriages". That one was a interview I got through a business contact who had a friend that needed database and website manager Te were chit chatting about the company, and he started talking about this and that and the topic came up. Should have told him I was trying to ditch my US citizenship, he would have had a heart attack.

-- A common one in the last 5 years, my MS. Which has shown up as "we don't want you flipping out on the clock" to "We don't need a retard on the clock" to "What happens if you drop dead on the job?" and my favorite "I don't want to catch your disease."

I have since took to carrying a hidden pocket recorder to all job interviews and contract bids. Right now though, it's mostly "We'd love you hire you, but we're cutting hours" or "This location is closing in <insert time frame> and we don't need cashiers we need a tear down crew"
Damn, I really don't blame you there, sounds like you've had some epically shitty experiences.