Another example mentioned is "bash". On the one hand, it has the meaning of to strike heavily, to criticize harshly (source), as in "Bashing Hillary? Don't go there, GOP". On the other hand, the word "bashful" means shy, timid (source). How could you justify these two opposite human behaviors with one single word (or word with a suffix)? This word, though, is different from "sanction", in that "bashful" actually has a completely different etymology and is related to the verb "abash", to make ashamed or embarrassed (source). In any dictionary, when two words have the same spelling but are descended from two etymological sources, they're usually listed as two headwords or entries. In case of "bashful", it's not the word "bash" with the suffix "-ful", but was formed by "abashed" + "-ful" and later lost the initial unstressed vowel (a process called aphesis). "bash" does have the same meaning as "abash" except that sense is now obsolete.
Well, some words that look like having different meanings but they don't, such as "flammable" and "inflammable". That's another topic, for now.