This was a surprise to me. Maybe because it's a mostly light-hearted comedy so I didn't take it too seriously, or maybe because it doesn't update frequently enough for me to remember the details, but I don't recall any foreshadowing. They did explain in this chapter that his inability to use magic and ability to see the chibis are hints, but the author never gave enough world-building lore that would lead a reader to this conclusion. There was nothing that said "he's a spirit" that couldn't also be explained by "he reincarnated in an isekai."
Still, it's a good twist, and I'm curious how it will go from here.