One small study found that coffee may damage the gastroduodenal mucosa in habitual coffee drinkers - http://www.ncbi.nlm.nih.gov/pubmed/15841908

And another found associations between coffee consumption and inflammatory markers - http://www.ncbi.nlm.nih.gov/pubmed/15447891

One AS patient reported a remission of symptoms after giving up coffee and alcohol - https://www.kickas.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=471446#Post471446