@allam, yes, your web server doesn’t include the intermediate cert, well, it includes one intermediate certificate but not the right one, you are serving the intermediate certificate for Let's Encrypt Authority X1 but you should include the right intermediate cert that in your case is Let's Encrypt Authority X3.
Edit: I think you are using IIS so maybe you are suffering a caching problem and your IIS is still serving the old X1 intermediate certificate, if that is the case, this thread could be useful to you IIS 8.5 building incorrect chain with Lets Encrypt Authority X3 and this post provides a solution IIS 8.5 building incorrect chain with Lets Encrypt Authority X3
I hope this helps.
sahsanu