Yes you can be cut after a reference check, good, bad or otherwise. They may have more viable candidates than positions. Obviously in that case it's possible to be rejected even after a good reference check. Just like any job, they will take the best candidate for the job, and that may not be you.
Candidates have also been unsuccessful during ground school as well, it's by no means certain that you have the job until you are checked to line and pass your probation period. Anytime in the first 6 months you can be unsuccessful. Something to keep in mind.
