It doesn't really matter how much work you do before you save your progress. All that matters is that you need to restart that application after every save. Thats all. That cave which is more than 50 times there - thats exactly that duplication bug. From 1 are 2, from 2 4, from 4 8... 16, 32, 64, 128, 256... and enjoy deleting
. This, on the other hand, happens when you are not saving the whole edited area together (or a whole map, if that is possible due to small-enough map being used).
About those versions, that sounds quite strange to me. I have no explanation for that, but what I wrote should prevent other such errors from appearing again.