I've been workin on a lvl but for some reason whenever I Save&Run the lvl sometimes events and tiles r missing. Also unwanted tiles appear in the game but they aren't shown in any of the layers in JCS.

Check all removable blocks,(destruct, trigger, stomp) and MAKE SURE they are an animated tile. You can do this by turning all animations used for this purpose off of speed 0. Any destrct/trigger/stomp tiles that aren't now flashing need to be replaced.