User blog comment:Miskos3/Fairy Tail Chapter 334: Sin and Sacrifice, Review/@comment-904888-20130607123637/@comment-7418318-20130607145455

Arc of Time can affect organic substances and has been able to from the start. She was able to make a seed grow into a tree and restore the Tenrou Tree.

In the past Ultear was unable to use it on animals and Humans, but at some point during the three year timeskip she managed to "evolve" her Arc of Time.

She used those evolved powers to unlock Second Origin in Natsu and Co, so now she can clearly affect Humans with Arc of Time, at least in some ways. With her not exactly elaborating on how this seeming "violation of rules" was possible, we have no idea of the extend of her powers after the timeskip.