DRAFT - this needs editing
Firstly, degradation of the gut wall by an invasive pathogen. This allows antigens and even whole pathogens entry into the body proper via blood and/or lymph. This is highly provocative to the immune system and this alone is enough to create serious disorder and pathology. The main contenders here that I am aware of are H. Pylori and, of course, fungi such as Candida.
Secondly, we have Molecular Mimicry. Many pathogens have learned to evade our immune system by imitating specialised receptors on the surface of our human cells. These receptors are what our immune system uses to differentiate the self from the invader, and by copying these structures our immune system is made a fool of and becomes ineffective. The dampening effect here would mainly be handled by T regulator cells.
But nothing is absolute, and this regulatory system can fail at times. And when it fails the result is a catastrophe. As when it does recognise the invader, based on other chemical signatures, the immune system may be unable to fully dampen the immune response triggered from the invader. In this scenario parts of the immune system will now see those areas of the body which also resemble the invader as foreign. Now in an attempt to clear the invader the immune system will also attack those parts of the body which carry the same receptor. This is what we call an autoimmune disorder.
Thirdly I would like to point out some things about our bodies Eco system. There are many adverse environmental factors which are causing harm to our commensal flora - that 'beneficial' flora which is protective towards our continued good health. These environmental factors can be split into two broad categories: those which kill the normal Eco system, and those which inhibit the transfer of beneficial commensal flora to our bodies. Consider the following: antibiotics, food preservatives, antibiotic hand wash, modern sterilisation of all forms, and lastly soil microbial systems have been devastated by modern farming techniques - soil which would in the past have been a natural reservoir for commensal flora, with our food being an intermediary means of transfer to ourselves.
And them there is stress.. But that is a whole other story (perhaps see my post in May 2015 for something relevant).