Misrepresentation requires two elements:
1) Incorrectly stating or improperly omitting a fact (aka lying when asked a question)
2) the information improperly provided could have led the visa officer to arrive at a different decision
Your story of you pointing out to the agent that the sibling was missing and the agent saying "too bad" isn't going to solve (1) above. But it may not be a case of (2).
You still need to inform IRCC of this issue when you next apply. If you next apply for something and include a letter of explanation saying "we told our agent to include my sibling but the agent said too bad" and it turns out that the agent actually corrected the file, it won't matter. If the sibling was not included, and you include a letter explaining this, it's also not too much of an issue UNLESS the sibling would somehow render you inadmissible.