Can you provide an example?

We cannot fix broken email clients. A workaround could be to encode ) as ) in HTML formatted links but that still won't solve the problem for messages sent as plain text.
I'm going to close this ticket as a duplicate, see T40265: Links in emails: Parentheses ( or ) not recognized as part of URL - brackets should be URL-encoded.

Only the closing paranthesis at the end of the URL is affected, not the opening one inside the URL. Therefore I do not think, it is caused by URL-endocing (unless the opening paranthesis gets encoded and the closing one does not).

Also I do not think, that it makes a difference if the mail is HTML or plain. Either the mail client will support URLs in plain text mail - then URL encoding will work. Or the mail client does not, then you have to copy the URL and paste in the web browser - in which case an encoded URL will work also.

In T207405#4679456, @C.Suthorn wrote:

Only the closing paranthesis at the end of the URL is affected, not the opening one inside the URL. Therefore I do not think, it is caused by URL-endocing (unless the opening paranthesis gets encoded and the closing one does not).

It is the very same technical problem: Email clients trying to be smart while they are not. It can be solved by the same workaround: Using URL encoding.

In T207405#4679474, @C.Suthorn wrote:

Also I do not think, that it makes a difference if the mail is HTML or plain.

It does. A link in plain text is just plain text. The URL is exactly the text.
In HTML format, a URL can have a link text instead. Like this where the text Like this is not the same as the URL https://wikimedia.org.

I have copied two lines of a mail from the file I saved the mail to:

see <a href="" onclick="parent.phx.event.mailUrlClicked(&#39;https:&#92;/&#92;/meta.wikimedia.org&#92;/wiki&#92;/User:Xyz_(WMF&#39;); return true;">https://meta.wikimedia.org/wiki/User:Xyz_(WMF</a>) for the<br/>

<a href="" onclick="parent.phx.event.mailUrlClicked(&#39;https:&#92;/&#92;/meta.wikimedia.org&#92;/w&#92;/index.php?title=User:Xyz_(WMF)&amp;action=unwatch&#39;); return true;">https://meta.wikimedia.org/w/index.php?title=User:Xyz_(WMF)&amp;action=unwatch</a><br/>

Adding "&action=view" might solve the issue.

That's another workaround, correct. Adding &whatever=whatever would also solve the issue. :)