When URLs are auto-linked, we never include a trailing period (or comma or question mark etc.) for reasons that are very obvious in your question. However the change to improve auto-linking around trailing parentheses is made in such a way that the closing paren is first included in the to-be-linked URL, only to be excluded again if we find that it has no matching opening paren inside the link.
This exclusion of the trailing paren obviously changes the character that ends the URL, so in this case we have to check again that the new trailing character (in your case, the period) is still a legal character to end the auto-linked URL, If it's not (as in this case), it has to be excluded as well.
This is fixed in both versions in the next build. I realized while typing this answer that this still isn't quite right, since it fails to handle situations where more than one such trailing character ends the url:
(y u no http://google.com???)
– I'll fix that as well. That's a much more rare edge case though.