OK - while I cannot reproduce this, there is an improvement I can make with the "Hide ignored quotes" setting that moves the removal of the quote to the back-end processing instead of front-end Javascript, and that will be in the next version of the application.
I also do not see any issues like this - test it out on the new version when it is available, and get back to me if still a problem (I will need some reproduction steps, in a clear format, to follow)