Nice topic to discuss Ahmed,
If you are using some plugins to handle them, the filtering logic that they keep updating might have some kind of semantics that block the original and genuine comments too. If suppose someone what's to post a comment like 'Nice post man! Keep bringing in more like this.", it would still be considered spam by some plugins and is flagged.
What I suggest is not to install any plugin if you are not getting that many spam comments (which is not possible these days) and if you had to buy the premium version of it to get the full benefits of its functionality.
To check manually:
No spam comments will read your post and respond. That means he won't comment about the specificity if the posted content. Beware if the link leavers. They don't actual mean to comment genuinely but wanted to gain similar backlinks.
The manual filtering of the comments will come by experience. All the best!