The Vision's (Mind) Infinity-stone came from Loki's scepter which came from the Chitauri, so it was well away from Earth, brought to Earth by someone with plans for all the mind-stones (Thanos). It was only very recently on Earth.
The Tesseract (Space-stone) was hidden on Earth, presumably by Odin, for safe keeping. Taken back to Asgard when it was no longer safe on Earth.
It's worth pointing out that safekeeping can be done under heavy guard or it can be done by simply hiding something. The Tesseract on Earth for centuries, and the stone in Guardians-1 (Orb or Power-Stone) weren't guarded well at all, just hidden.
The Origin of the Eye-of-Agamotto in the cinematic universe wasn't made clear but presumably the first sorcerer supreme, Agamotto, who is mentioned in the movie, knew what it was.
So there were likely 2 stones on Earth for some time, Tesseract and Agamotto, which fits your question, one hidden, one protected in a magical sanctum. What's not clear is whether either keeper/protector of each of those stone knew of the other. It's not something anyone is likely to advertise, so Odin and Agamotto may well not have known of each other's stones.
When Shield took Loki's scepter and stored it in the vault, it's unclear if Thor knew it was the mind-stone at the time. Dr. Selvig might have suspected, but it's unclear how much he knew about infinity stones. If it was known that the scepter held a stone after Avengers-1, and it's not clear that it was known, but if it was known, the thinking at the time could well have been - one stone under Shield protection, one back to Odin's protection.
Thor had a vision of the stones in the sacred water in Avengers-II, but precisely how much he knows about their location isn't clear, so it's still not clear if anyone other than the sorcerers know the location of the time-stone.
The risk with Odin's thrown room is that, even under guard, it's fairly common knowledge that it was full of juicy loot. The feeling might have been that such a high profile vault shouldn't contain two stones, especially since one is fairly well known to be there after the events in Avengers-1. If the stones are better hidden, Agamotto for example, that issue might not come up.