When you install the Lets Encrypt SSL it has to validate the domain name and it does this by creating a folder called '.well-known' at the root of your website. By default, any request and Lets Encrypt is unable to get to the folder and the validation process fails because of the way Umbraco manages requests.
To fix this you need to modify the web.config of your Umbraco website. Update your web.config from
<add key="umbracoReservedPaths" value="~/umbraco,~/install/" />
<add key="umbracoReservedPaths" value="~/umbraco,~/install/,~/.well-known" />