Are you using InDesign’s paragraph composer or single-line?
The paragraph composer really does a good job.
And even though it does, it won’t be perfect, and sometimes one will still have to tweak a line here and there.
Personally, I never have the preview on, as I can judge by eye what looks good and what doesn’t. And when it’s turned on, you can go crazy just looking at it and worrying about getting rid of them. If you prefer to use that feature, just remember that it’s only a guide as to spacing violations per InDesign and the settings you chose. To be honest, you will see a violation no matter your settings. One paragraph will be fine, but another may not. (Not the entire paragraph, but lines here and there).
What settings are you using for your H&Js? In the books we do, my normal settings are:
Minimum: 85 / Desired: 100 / Maximum: 150. Sometimes I will change those a little depending upon the font.
For the hyphenation I allow 3 up, 3 down, and 2 hyphens in a row maximum.
Maybe try those settings and be sure to have paragraph composer turned on in your style sheets.
And personally, I’d turn off that preview feature of H&J violations.