Any number of things can cause the BER to be disturbed. Bit Error Rate basically tells you the number of erroneous bits that failed to reach their destination. Be it ingress, a kink in the cable, or a bad fitting, any of these things will disrupt the proper flow of information.
When reading BER, there is both pre and post BER. Pre is the number of bits before error correction, or the resending of bits that were disrupted. Post BER is the number of bit errors after error correction, meaning that if the post BER is correct (1.0E-9) then any bits that were interrupted were successfully resent and the data arrived in whole. Ideally, you would like both pre and post to be identical, but it is primarily the post BER that you are concerned with.
Troubleshooting still consists of divide and conquer. If you have a bad BER at the box, then backtrack and remeasure until your BER is up to par and repair accordingly.