EDIT 2016-07-04(Since this question is getting popular): This is a bug in Chrome. Developers are actively working on a fix.
EDIT 2017-05-14<
A suggestion from a related discussion solved the issue for me: https://stackoverflow.com/a/46117022/7375996
Using calc with some offset solved the issue in my case:
transform: translate(calc(-50% + 0.5px), calc(-50% + 0.5px));