The influence of loan words on English give vastly different pronunciations of words even regionally. For extreme examples see "shibboleth", especially in the UK.
What I've found with some cursory googling is mostly place names, which I agree often have major differences between spelling and pronunciation. Even there, many of the examples on the Wikipedia page are still plausible spellings for the pronunciation, especially given how ambiguous English spelling is in the first place. Others seem more like nicknames that have essentially replaced the original full name of the place, while the full name is conserved in the spelling.