Colonel is like that because English and French have a messy history and we refuse to change either the spelling or pronunciation to fix it. French took the word "colonello" from Italian and adapted it as "coronel", English took that version and pronounced it poorly. Scholars tried to re-align to the Italian origin by spelling it "colonel" but nobody changed the way they said it and it's been that way for over 400 years.

In British English they pronounce "lieutenant" as "lefftenant" for a harder to trace, and presumably stupider, reason. When an English word doesn't make sense it's probably because it came from at least one other language and was adapted just enough to fit the phonemes.