The word contronym (also the synonym antagonym) is used to refer to words that, by some freak of language evolution, are their own antonyms. Both contronym and antagonym are neologisms; however, there is no alternative term that is more established in the English language.
apology - admission of fault in what you think, say, or do; formal defense of what you think, say, or do
by - multiplication (e.g., a three by five matrix), division (e.g., dividing eight by four)
consult - ask for advice, give advice
deceptively smart - smarter than one appears, dumber than one appears
dollop - a large amount, a small amount
first degree - most severe (e.g., murder), least severe (e.g., burn)
flog - criticize harshly, promote aggressively
give out - produce, stop production