If the customized product thumbnail is not displaying in the WooCommerce cart, it could have several reason.
Solution: Disable Lazy-Load
There are some plugins like "SG Optimizer" who are having a feature to enable Lazy-Load. In that case the plugin is replacing the cart thumbnail again. You need to disable Lazy-Load.
Solution: Change Theme
Depending on the templates structure of the theme, the customized product thumbnail can not be displayed. Please try a different theme. If the theme is the problem, we can not do anything in that case, because then the theme is using some custom structure that is not standard defined by the WooCommerce coding codex.