A few reasons. One is that most spellings in common words in English became largely fixed during the Middle English period, and in the transition between middle and modern English the way the language was spoken changed significantly. Letters that were pronounced in Middle English fell silent in Modern English, or changed significantly the way they are pronounced.
For example “knife” was actually pronounced with the k and the e sounded when the spelling was fixed, but then people stopped pronouncing those.
Another is words entering English from a non-English source retaining the spelling of the source language even though the normal way English words are spelled would imply a different spelling.
For example, “cassette” has the extra te on the end because that’s how French is written, even though an English word “casset” would have the same pronunciation
In a few cases, words that came from a non-English root (or were believed to come from one) had spellings deliberately changed by scholars who wanted to the spelling to reflect the source (or perceived source) of the word.
For example “debt” was spelled “dette” or “dett” in Middle English, but scholars recognised it was related to debitim in Latin, so added the pointless b into it. This particular method is how the s in “island” came to be.
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