I might be thinking of some of the cache timing issues about sharing physical hardware with other guest VMs. There were papers in the last two years showing circumstances in which another VM on the same device can learn about secrets in caches via timing experiments. But that's a cache issue rather than a general pipeline issue. So I still can't remember if there's something else that I'm thinking of or if I'm just confusing it with the cache stuff.

http://blog.cryptographyengineering.com/2012/10/attack-of-we...

More recent stuff in this vein:

https://eprint.iacr.org/2014/435.pdf

(Yikes!)