So in order to get the achievement you must clean everything from the map. Once you have cleaned the things that you are able to see and what not, you will think you are done. However, sometimes the game bugs and the beepers will still be going, usually the blue one (blood).

When you find the location of the stain (it could be invisible) with the high frequency beeping, you can simply type in the console "killnearestmess" and the beeper should revert back to normal and voila.
NB: Console can be opened by pressing the button ` (above TAB on PCs).

Hopefully it works for you guys as well!

Suggestion from Seriox to clear it even quicker:

Just open console, type "setbind MouseScrollUp killnearestmess" and "setbind MouseScrollDown killnearestmess". Then scroll your mouse wheel up and down for 30 sec. (I have not tested this).