Files in sub-folders showing at top level

I don't think I have set something odd - but, like the subject says, Files in sub-folders showing at top level.

Thus, files in my Images folder also appear in the top level - but when I try and download them, or view them, or delete them, I am told "No such file or directory". So are they there, or aren't they?

This is not good, as I easily get confused! :?

All suggestions gratefully received - even if it's my fault.
Peter Royle