Shot myself in the foot

Two years ago I worked at a call center for $7 an hour because I couldn't find any other job. Most places said I was over-qualified, but the call center was desperate and hired me within an hour of setting foot in their door. I worked there for about 6 months, about 50-55 hours a week, coming in at 5 and 6am whenever they asked me to, and worked on my days off. When I left to go work for the airline, my sister began working there and was told that I was the best employee they've had.

So it confuses me that I received this letter of feedback from Radford when I asked them for suggestions on how to improve my job search. (Byron Bordelon is the boss at the call center):

Good Morning, Ashley.

Actually, you did a great job with your telephone interview and we
seriously considered inviting you to campus for a second interview.
However, we had the unique experience of having multiple viable
candidates (six) and in light of our time constraints, had to narrow our
choices. We not only utilized our rating system based on the telephone
interview and needed experience, but we also took into consideration
reference feedback.

While your application was initially strong, it was within that
secondary process that your application was not selected.

The one suggestion I would make that could potentially strengthen your
employment opportunities in the future would be that you consider
granting permission to speak with your current employer as part of the
reference process so that Byron Bordelon from Nationwide Response/Call
Center is not contacted for information. I'll not elaborate on that
suggestion, but I think you'll understand its implications.

Best of luck with your future job search.