I have line numbers off in preferences.
This is ignored and line numbers are shown when opening new html, js, css files (probably others). Doesn't seem to affect .py files.
Only way to get rid of line numbers is to right-click on line numbers in context menu after opening new file. (Strangely, this doesn't do anything first time, but works after right-clicking and unticking line numbers at a second attempt.)
After closing a file, when opening it again the line numbers are back.
I was using 3.0.5 before and this was not a problem.