If you are working for an organisation, and you say that you feel like a square peg in a round hole, what you mean is that you feel like a total misfit. You and the others around you sense that you don’t belong there. The expression can also be used to refer to someone who is unsuited for the type of job that he/she is actually doing.
Example: I’ve always felt like a square peg in a round hole in this university. I think it’s about time I resigned.