I noticed that my hacker's Drone Puppeteer skill wouldn't increase properly after installing the newest patch. You could spend skill points on it and it would never increase, but would actually disable the skill completely like you didn't have it anymore. I'm not sure if any other skills are affected.

If you run into this issue, just clone the affected agent into another body before you attempt to level up the skill and it'll work properly.

I just wanted to post the work-around in case anyone else ran into this problem.

I haven't got a chance to test out the new patch yet.

I have suspicion that the bug is due to an old saved game format. I was poking around in the saved game files, which are just plain text XML. I got the idea that cloning the broken soldier might fix the issue, since it should replace the XML object for that unit and fix any broken entries, and it worked. :D

I did send in a bug report to 5 Lives Studios along with my saved game a couple days ago, so they should know about it eventually if they didn't get to it in this update.