Had created an outpost with 2 shards just outside it's zone of control (going to high tower it once I have researched the tech), after loading a save, the shards are not displayed on the screen but the tool tip appears when I hover the mouse over the squares where they are.  I have a save if you need it.

I also had an issue earlier in the game where a pioneer I was moving disappeared from the map, the counter for the unit still appeared down the side of the screen and when I clicked it the map focused on the location the unit had been in but when I tried to right click a square to move the invisible unit nothing happened, saved and reloaded the game and the unit was back again, below is a screenshot of the location that the Pioneer disappeared:

Loving the game, had that one more turn feeling last night and ended up playing till 5am.  The game looks beautiful as well, you should all give yourselves a pat on the back.