City building
(note I do not know how to reproduce this but it happens all the time to me).
For clarity I want to define two terms I will use: City improvements are those improvements attached directly to a city on the grid (e.g. workshop, study). Resource improvements are the improvements built on one of the resources (e.g. gold mines, farms).
As far as I can tell, the city improvements are fine. However, when I build a resource improvement, usually they do not show up in the city building queue and are built in parallel with a city improvement. It may have to do with whether or not a city improvement is already building when I try to build the resource improvement, but like I said I have not tested it.
Read the excelent post regarding city improvements and how resource improvements work (something with City Limits).
The fast answer is that when a resource tile is next to a city, it gets enclosed in the wall. From then on it's part of the city for all purposes. Defended by the city units, takes up 4 spaces from the city, extends the city limits AND is in the build queue for the city. So, this is expected behaviour, just not explained anywhere in game!