It's not unusual for it to separate a little as it sits in the fridge, and it should come back together pretty easily. I've never seen it separate while I was eating it, though. That does seem odd. I'm not really sure why it's doing that or how to prevent it.
When you make it, are you using an immersion/ stick blender, or whisking by hand, or something else? If you're whisking by hand, maybe it's not completely emulsified? (I think it would be harder for this to happen with an immersion blender or mixer, but I might be wrong.) You also want to be sure you don't add too much oil, and this depends on the size of the eggs you're using, so if your eggs are a little smaller, you may not use the entire amount of oil the recipe calls for.