I am having a similar issue with stealth currently. I was playing on Ivara to do some Simaris rep after finishing Sythesis and I noticed something strange. While invisible, if you use your scanner (not even after a complete scan, just using it in general) Will alert enemies to you, and cause them to run up to you and stand there like they want to shoot at you. I even had one enemy circling around me in my face. This obviously makes stealth scans impossible unless I put them to sleep first. It's like the scanner itself makes noise now so it alerts everyone in the area, but it feels more like you completely aggro them but they can't shoot because you're invisible.