When I click on the icon with the green arrow to show only files to copy from left to right, then click on "synchronize" and then, during synchronization, click on the icon with the blue arrow to show only files to copy from right to left, synchronization carries on with copying, but then with the other files. Happens also with all the other icons used for filtering the shown files. Should be easy to reproduce, otherwise ask me for more information.
My solution would be to disable the icons (and the corresponding entries in menu, too) during synchronization to prevent from copying files not intended to be copied.