All of things in spawn chunk reset in some conditions

All of things in spawn chunk are reset. It's hard to describe. I was making map making technics by command blocks, and all in the spawn chunk blown when I start this map again.

Summary : JUST RESTARTED THE MAP, AND ALL IN THE SPAWN CHUNK BLOWN.

Screenshot 1 : While activating this map. I was making custom /clone command. No size limit, include rotate/mirror functions, but slow. It clones progressively, and randomly. It was activating over than 100 commands per tick. (include execute individually)
Screenshot 2 : Before restart the map.
Screenshot 3 : AFTER (All hopper clocks disappeared)

p.s. Also there are similar bug that some world(not ALL worlds) before 15w36a is not compatible with after 35e.
p.p.s. I don't know about deep programming knowledge. I did my best to describe.