Does this phrase mean "When you cause a problem, people get upset."?
2 Answers
It means that actions have consequences.
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Who else is out on the pond, and what is lurking under the surface? Commented Dec 24, 2014 at 13:24
"Don't rock the boat" is a well-known (in the US, at least) phrase meaning "Don't ask too many questions or be too assertive," lest you cause your current endeavor to fail.
Adding "there will be waves", while not a common expression, is readily understood to mean that "rocking the boat" could not only damage the current endeavor but could cause consequences that would affect you directly.