It's really not so much writing-related as language-usage related, but since writers use language as their weapon of choice, it might as well be labeled as a writing-related post.
1) literally - did you know that a kitten dies every time someone says or writes "literally" when they mean "figuratively"? ;)
2) indeed - academics overuse this
3) begs the question - it doesn't mean what you think it means
4) utilize - when the simpler, less pretentious "use" is often the correct form
5) theory/theorize - when people actually mean "hypothesis/hypothesize." A theory is a well-tested hypothesize that is supported by an abundance of empirical data. A hypothesis is just an idea...more often than not thought up on the spot. E.g. Someone spies a squished frog on the pavement and tells his friend, "I have a theory as to how this happened." Um, no; you have an idea, a hypothesis. You've not tested this thoroughly; it's not a theory.
6) at the end of the day - just an awful cliché
What are some other words or phrases you've noticed that people use wrong or too much? Please share in the comments!
"I may not have gone where I intended to go, but I think I have ended up where I needed to be." ~ Douglas Adams