I've only noticed this issue on the Railway and Portable Solar Panel techs, and is not there for Logistics Robotics (which also has 3 follow-up techs).
http://i.imgur.com/iFWqVZW.png
As shown, the central follow-up tech icon has the connecting line shift 1 pixel to the left.
[15.3] Tech tree lines sometimes misaligned by 1px
Re: [15.3] Tech tree lines sometimes misaligned by 1px
It's nearly impossible to get rid of all these cases where two technologies end up one pixel off of perfect alignment. You'll have to live with it.