[SmartCrawl Pro] Posts and pages gradually getting no-index

I noticed in the Google Search Console, that for the last months more and more posts and pages on the website are getting no-index setting. SmartCrawl is globally set to index all pages and posts and I never override that on any page or post I publish, but still when I check some of them, they have the Index – Override Post Type Setting disabled. And it's like that on ~500 out of ~1000 (31.07. = 349, 15.08. = 545), so cannot enable that manually. Any idea why has this happens and how to fix it?