
There are many datasets that can fall into this category - for example, there have been several publicized cases involving the misuse of GIS tax parcel mapping to attempt to enforce such things as building setbacks and other ordinances, to the harm and detriment of property owners who may in retrospect have actually turned out to be in compliance with the ordinances - though in some instances only through costly litigation and/or demolition of a structure. In some instances, actual surveyed boundaries were rejected by undereducated GIS staff or other bureaucrats, in favor of digitized-and-rubbersheeted GIS parcel boundaries or misused COGO routines in the hands of people who do not have a solid understanding of surveying. Clearly this is unacceptable misuse of GIS data.
Among other things, I work extensively with GIS data for facilities, which may contain toxic or hazardous materials - certainly agencies which regulate their activities and emergency responders need to have ready access to what is onsite, and what the consequences of a catastropic event at one of these facilities might be on the community - but aside from keeping this data from the hands of would-be agents of terror, certainly that facility's competitors might be able to gain some competetive edge from knowing what this facility is working with. This is generally known as "Confidential Business Information" (CBI). It is a classified data category apart from the usual Governmental Secret or TS/SCI classification hierarchies.
Another area with tremendous potential for misuse is in traffic incident data - Departments of Transportation collect information on reported accidents and incidents, and plot them on roadway maps - the analysis of this can help the DOT in triaging, prioritizing, budgeting and sequencing improvements to the roadway for safety. However, in the wrong hands, this type of data can also lead to litigation - "you knew this was a bad intersection, yet you didn't do anything". Often a DOT is aware of problems for many years, but given budgetary or organizational constraints may be unable to act on them in as timely a fashion as would be liked - and a multimillion-dollar court award or settlement is generally only going to take away money from being able to address the problem properly.

These are just a handful of examples - many more come to mind. GIS is, at the end of the day, just a tool. The ever-emergent plethora of geospatial data and the ubiquitousness of GIS tools available to the public is certainly wonderful, however data and a tool in the hands of one, either without the adequate domain expertise to use the data properly - leading to unintentional harm; or the intentional abuse by one who wishes to exploit the data toward personal gain at expense of the public, or toward the outright, intentional harm of the public, can be a dangerous thing.