I just got back into SimCity 2013 and am running into and issue as stated above with the Omega Co Factory bugging out, as is the Hydro Pumping Station, Fusion Powerplant, Sewage Sanitizer, Wave Powerplant. Something in the mods might be invalidating COT Buildings and causing them to break.
EDIT: Do you have any idea what program they use to edit these package files?
EDIT 2: Found Files that were buggin out. Pasted below:
Mod Parker Power Overhaul Fusion
MY MOD Wave power plant
MY MOD GroundScrubber
MY MOD Hydro pump Station
MY MOD Sewage Sanitzer
MY MOD Omega Factory OMG