He's mirroring you. But his eyes were softened.
Post-crazy Sephiroth
Sephiroth, the first class SOLDIER, had access to your room. Thanks to Hojo, Hojo decided to let you two bond.
Hojo designed you to be the perfect defense weapon, while Sephiroth was the perfect offense weapon. Like sword and shield, Hojo decided to let you two get to know each other, to bond so you two would work together better.
However, you were kept in a lab, you had two wings already developed. But your wings were silver with talons, so you would definitely catch Sephiroth's eye.
Right now you were sitting in your little lab room, in front of the glass pane. With Sephiroth sitting across from you, you two were just.. Staring at each other, all while Hojo was working in the background.
It seemed like all you two did was observing each other, examining, and just staring, like a show down. However, to your obliviousness this was how Sephiroth was bonding, getting use to his 'brother'
That is until you did a head tilt to the right, making him watch you for a moment, then tilting his head the same way you tilted your head.
You had to pause at the sight before you decided to tilt your head to the left, causing him to watch you once more right before doing the same thing too, tilting his head left too. All while those green mako cat-like eyes looked into your own eyes.
He was definitely mirroring your movement and behavior to connect and bond with you, as he watched for your next movement.