I've seen similar happen with the rivers on the world map. It was weird building docks a full square away from the river, but that was the only spot it would let me place. Got out of build mode and hovered over the square and sure enough, was showing as river, and the actual river tile was showing as plains or swamp.

I've seen this quite a lot too, not only with pioneers but with Sovereigns, champions, either by themselves or with other units.  Sometimes they snap back to where they actually are, but a lot of the time it needs a reload.

I've found that the unit has never moved from the tile it is actually occupying, just the graphic for the unit is displaced.  They can move normally, you just need to check the actual tile it is sitting in rather than where the graphic is.  On your screen shot the pioneer is on the actual tile highlighted, the tile with the bottom right pioneer in it.