Gordie,
I'll assume you're referring to the silo shaped tower in the location where you want to put a more realistic water tower. This isn't really an error in the autogen, it's more a coincidence. Landclass and autogen in the sim is not an exact copy of the real world. That would require many more GBs or TBs of disk space. In any case.......
There are 2 free programs that will allow you to remove the autogen object. They are....
-Airport Design Editor (ADE9X) which you can download here-
http://www.airportdesigneditor.co.uk/ -
-SBuilderX which you can download here-
http://www.ptsim.com/index.php?option=com_content&view=article&id=52&Itemid=56Either allow will allow you to remove the autogen object. I would suggest ADE9X for now as it is an airport editor if you ever wish to edit airports. Also it's help file is much more robust than SBuilderX. The drawback is it generates an airport file which might be undesireable if you every wish to share your work.
Note: If you do want to investigate SDK documents, the file Gary pointed to is also found in your SDK installation folder, ......\Flight Simulator X SDK\SDK\fsxsdk.chm.
Dave