This is the post I am taking about.
https://www.8theme.com/topic/limited-or-out-of-stock-after-cart-update/#post-359784
I have contacted to woo-commerce support and they suggested a way to test it in order to find the main problem. I tried deactivating plugins and shifting the theme, so what happening is if I disable all the plugins except Woocomerce and shift to the storefront theme the error got fixed, and when I shift from the storefront theme to Xstore we required a plugin called Xstore core right after activating Xstore core plugin again it starts showing the parent item but not the variation.