This happens when using center square ore setting with all other settings being default. It doesn't apply to the the starter hex core. This happens when the hex core spawns on the hexagon. The core spawns 1 tile too high in comparison to the ore, covering the ore under it. The difference between the starting hexagon and the others is also the hex core. The ore is the same distance from the bottom in the starter and the others.

That seems to only happen in some hexes, and most appear to be fine. I haven't come across that yet in my testing interestingly enough. But I see it now that I'm looking for it. The first four hexes with ores I look at were generated fine, but the fifth was slightly offset like you described. If it's always just off by one around the hex, then it's not a game-breaking bug since mining drills can still reach them under the hex core, but I'll look into correcting this generation mode for 1.0.17.

It's fixed for 1.0.17.