"Flammable" and "inflammable" mean the same thing. (Not quite what you were asking, but it's in the spirit of the question, I think).
"Literally" is often used for emphasis, even when something is figuratively but not literally true.
"Enjoin" means both to proscribe and to prescribe.
"Sanction" is similar; it's either a penalty for breaking a rule, or official approval of something.
"Dust" (as a verb) means both to clean dust off of something or to spread dust onto it.
"Fast" means fixed in one place or moving quickly.
"Oversight" means watching over something carefully, but also a mistake caused by a missed detail.
"Cleave" means both to cling/adhere and to split/sever.
"Hold up" can mean support or hinder.
This list can keep going. It's just the point that I got tired of finding more listicles to pull the best bits out of.