Seems like a bug, as usually the only parts of the map you cannot build on is the road, the very edge of the map and water.
Save your game and open the save file in a text editor. You can locate the map tile in the file using the X,Y coordinates and see what it says is there.
For example here are the first few tiles in one of my save games:
BEGIN "0 0" Mat PavingStone Con 0.00000 END
BEGIN "0 1" Mat PavingStone Con 0.00000 END
BEGIN "0 2" Mat PavingStone Con 0.00000 END
Mat is a keyword for material, in this case they are paving stones.
Con is the condition, or how much damage it has sustained; 0 means undamaged and 1 means it has been destroyed.
Find the cells you cannot build on and add the info to your question. Then you can edit the save file to change the material and reload the game.