Totally making stuff up here... But since no one else has given a half-way intelligent or on-topic answer: You're probably looking at two or three different phenomena.

The first: in old times, the people who first encountered a place may not have known what it was called in the local dialect and just picked something to call it, which eventually became the norm, even after they learnt what the place's inhabitants called it. Place names may also have changed over time depending on official whimsy/stubbornness, e.g. Myanmar vs Burma.

Second: the original name needed to be phonetically altered for easier pronunciation, e.g. Koeln (in German) vs Cologne (English).

Third: a variant of the name was deliberately chosen to "fit" better with existing language structure. Mandarin Chinese for example has both pure phonetic names (e.g. Jia Na Da for Canada), but it also has country names that fit the traditional way of naming places. Country names in Mandarin are normally one syllable followed by the word for country (Guo), e.g. Zhong Guo for China. So you see half-phonetic names like Ying Guo (England using the "Ing" sound) and De Guo (Germany using the "Deut/Deustch" sound).