I just had this happen to me as well. This is what happened.
1) I set up a new wordpress site at a temporary domain.
2) From the temporary domain, I connected Jetpack to my WordPress account
3) I published my site to the real production domain and changed the domain name in the settings of WordPress
4) Whenever Jetpack would generate a short link, it would point to the old temporary domain instead of the correct production domain.
Luckily I caught this and then created a 301 redirect at the temporary domain for anyone that saw the short link.
However, here’s the fix:
Simply go into your Jetpack plugin settings, then “Disconnect” from WordPress.com. Then re-connect it again immediately. I think this forces Jetpack to read the proper domain settings again, and will start generating proper Short links to your blog.
Hope this helps.