There seem to be at least two issues here. Firstly, where a pilot falls foul of his/her boss and then finds that said Chief Pilot is giving them a bad reference through an informal contact with the prospective employer. Many of you, quite rightly I feel, have condemned such action. I knew of one such case and thankfully for the pilot concerned our new boss could see this embittered chap for what he was and so took no notice whatsoever.
However, a second and equally valid scenario is the one put forward by Devil's Advocate. Someone at the very beginning of this thread reminded us that professional aviation is a very small community within the UK. There is a very small number of individuals who will cause problems wherever they work and it is human nature that having built themselves a bad reputation it will spread to other companies.
Lastly, as slj said this 'old boy network' can often help pilots get jobs not lose them.