When you use /clear sometimes the item get removed but the icon of item still in the inventory (actually you can't use it & when u click on it all the fake icons gonna disappear)
When you use /clear then /give if the given item went to the /cleared slot it gonna be invisible (to make it visible again you need to click on it)
Please check if that's still an issue for you in the latest 1.15.1 stable release