Eclipse error constantly pops up while editing Javascript
An even better answer (from the bug report linked by Cliff Ribaudo, comment #10 and others):
Turn off Toggle Mark Occurrences (Alt-Shift-O or the paintbrush icon on the toolbar, which handily, will show you your current state).
Thanks Cliff!
Edited:
At first I thought this was just a trick, but it is working so well, I had to post it as an actual answer.
When the error window pops up, don't close it. Just drag it off to the side, focus back on the main window and keep editing.
When the error happens again Eclipse doesn't change the focus back to the error message. Focus stays in the editing window and you can continue to edit the document.
Likely an eclipse bug. See this thread:
https://bugs.eclipse.org/bugs/show_bug.cgi?id=359005
There is a patch posted there which you might try.