This excerpt below explains how some inaccuracies occur. In my experience, I have seen what may look like 300-600m differences in actual locations. As they say, accuracy is only as good as the data used,if there is a mistake in foundational data, this will eminate causing more widespread inaccuracies throughout a whole data set.

GIS uncertainties [edit]

GIS accuracy depends upon source data, and how it is encoded to be data referenced. Land surveyors have been able to provide a high level of positional accuracy utilizing the GPS-derived positions.[15] High-resolution digital terrain and aerial imagery,[16] powerful computers and Web technology are changing the quality, utility, and expectations of GIS to serve society on a grand scale, but nevertheless there are other source data that have an impact on overall GIS accuracy like paper maps, though these may be of limited use in achieving the desired accuracy since the aging of maps affects their dimensional stability.

In developing a digital topographic data base for a GIS, topographical maps are the main source of Aerial photography and satellite images are extra sources for collecting data and identifying attributes which can be mapped in layers over a location facsimile of scale. The scale of a map and geographical rendering area representation type are very important aspects since the information content depends mainly on the scale set and resulting locatability of the map's representations. In order to digitize a map, the map has to be checked within theoretical dimensions, then scanned into a raster format, and resulting raster data has to be given a theoretical dimension by a rubber sheeting/warping technology process.

A quantitative analysis of maps brings accuracy issues into focus. The electronic and other equipment used to make measurements for GIS is far more precise than the machines of conventional map analysis.[17] All geographical data are inherently inaccurate, and these inaccuracies will propagate through GIS operations in ways that are difficult to predict.

http://en.wikipedia.org/wiki/GIS_software