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Check out the link profile of the site whose links Google doesn't like
with many cases i saw, they are marking valid backlinks as spam
If you are satisfied that the links are genuine and the site is genuine I'd try to let Google know that they've got it wrong. It's hard enough to get links without disavowing freely given ones!
All linking pages are subject to changing conditions upstream of them... anything from code changes to business changes to algorithmic changes, all of which can positively or negatively affect inbound link juice. Some pages have good enough content to attract inbounds once they become sufficiently visible, which can mask other upstream changes. In some market areas, links will be affected by upstream link buying and selling as well....
One of them even wrote a tutorial about how to use my site's app!
I surely don't see how many small businesses/webmasters can inspect the backlink profiles of not only their sites but also of everyone who links to them
Not for free, I'll grant you.
But in an eco-system where you are held responsible for your IBLs then checking your profile makes economic sense.
With so many "false-positives" lately, one has to question if Google is using its marketshare to scare webmasters into not linking to one another.
But the algo is still mainly based on links, so Google needs us linking.