Bug introduced in 10.0 and not fixed up to 10.2
At some random point in time the highlighting does not disappear any more. By highlighting I mean transparent boxes appearing for
- find feature indicating found object,
- cursor highlighting once you go back to previous line and
- bracket matching when one adds the closing bracket.
It does not start right away with a new notebook but appears on some random point. After this point in time every highlighting remains. They do not disappear on window resize, minimize, maximize or any other event I have tried to trigger. Only solution is to reopen the notebook.
I have observed the problem on number of PCs I use in lab all having different versions of Mathematica 10.0.x and Windows 7 or 8, 32 or 64 bit. It is still present with Mathematica 10.1.
I did look through all Mathematica v10 bugs reported here with front-end tags and I did not find it reported yet. As we have it on many PCs I must not be the only one experiencing it. Has anyone found a workaround, which makes the disappear?
I have not jet reported to Wolfram as I have not figured out a way of reproducing it. But for me and my colleagues here it happens daily.
Here is a screenshot:

Edit Now I see it has been reported before: Coloured marks appearing in notebook input text
Edit 2
The bug is still there in 10.2 although it did take me long time to get it again:

SystemInformation[]notebook for every computer where this happens and various screenshots. They can probably provide you with things you can try to narrow the bug down. – halirutan Jun 17 '15 at 11:19http://mathematica.stackexchange.com/questions/64102/colored-marks-appearing-in-notebook-input-text?rq=1
– Johu Jun 18 '15 at 21:52