Actually, I don't think they override an old one. I had, for example, a shard popping up on top of my already built farm. I've also seen shards showing up on top of other resources too (even AI's). When I click on them, though, old ones still exists and are still selectable (I could still select my old farm) but the new ones are not (couldn't select or develop a shard). Also, I've seen notable locations and quest locations showing on top of resources as well. In fact, I frequently saw more then one notable location on the same tile. When I get there, I would get 2 rewards from them at once. Shards in particular seem to show up at insane amounts. In my current game I have LOTS of each shard, many of them showed up around my cities before they hit level 3. I thought shard's are supposed to be a rare resource. ATM they multiply like rabbits.
One of the problems I saw with consistency is the fact that map does not update with new locations as soon as you get a research for it. Usually it takes some event to 'refresh' the map to make them show up. It adds up to the inconsistency feeling you get. OFC, there are some inconsistencies when you load a save game too. Not only does it appear that new resources/shards show up but some of the items that give bonuses (like increased movement) don't work when you load a game until you hit the end turn button. Basically, if you have a hero with a ring of stamina that gives 1 map movement point so he has 3 instead of 2, when you load a save game, he will have 2 and will get 3 only after you hit end turn button. This may be true to other item bonuses as well, but most are hard to test.
Also, apparently most of the OOM messages pop up when you try to save a game which means that saves are one of the causes of memory leak so it just adds up to the total feeling of save game system broken. This really, really, needs a fix. A solid and reliable save game system is a MUST for any game, even more so for a turn based game.