I have made a recording about the problem just to fix it properly because there are 2 issues with it:
-the first product in the video, on the store front, it shows that it has 21 different colors , but some of them are not available but it shows on the store front instead of hiding the unavailable colors... BUT if you click on it, as I did in the video, then you see, it shows on the product page only the AVAILABLE colors , there are 14 available colors on stock.
-the second product on the video has much more variations, on the store front it shows 31 different colors , both unavailable and available colors, same issue, BUT if you click on it , as I did in the video, you can see that it shows again all variations on the product page, so all 31 colors, both the available and unavailable ones also...
so there is an issue that it shows the unavailable colors on the front store page instead of hiding them and there is an another issue probably something limit issue because if it is more than 25-30 variations then on the product page it shows wrong also not only on the front store page...
check video just to refresh memory:
https://www.dropbox.com/s/bnx23gsupye2oz0/colors_upd.mov?dl=0
Thank you Yame.