Cloudy water due to sediment stir-up will not hurt your fish.
But we need to figure out what's going on. Here are a lot of questions that would be helpful to have the answers to.
How long has your tank been up and running?
When you did your major cleaning how did you clean your filter?
What were the steps in your major cleaning?
Does the cloudy water look like mud or milk?
How quickly did it cloud?
Did you heavily stir up the gravel while cleaning?
What kind of gravel do you have? If it's an aquarium soil did you rinse it before adding it to the tank?