Yes, it does appear that Surtidor Shell Antiguo is the Wayspot for the L17 S2 cell that the gym is actually in, and Calavera Negra is in the cell to the east, so even if the gym was approved, it wouldn’t be eligible to be a stop/gym in PoGo.
It may be possible that staff thought you were trying to purposely misplace the gym, but I find it somewhat odd since the cells here are occupied. Here’s what they look like for reference: