The Gemara discussed a machlokes if the partial word (small word from larger one) consists of two identical letters. Rashi in the Mishna seems to say that if he intentionally wrote a short word consisting of two identical letters it is a melacha. What is the difference between these two cases?
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Perhaps we can say that surely a word of two of the same letters is not any less of a word than a word of two different letters. However, when you had in mind a different word, which includes in it smaller combinations of letters that happen to be a word, you will only view it as a word when it is from two different letters.
In order to break from the category of being merely a component of a word, and be seen as a word of its own, it has to have its own components. Two of the same are too innocent looking to be taken for, or thought of as, a word when you were actually trying to write a larger word.