It has been pretty clearly established that Apple keeps a never-ending log on the iPhone of a users comings and goings which leaves users vulnerable to their device revealing their activities to parties like customs officials, jealous or abusive partners, random police at traffic stops and basically anyone who can get their hands on your phone or PC for a few minutes.
Despite Microsoft coming forward early and clearly stating it only kept a single location on your phone until replaced by the next, unlike Android which keeps 250 records (about 3 weeks worth) and iPhone for at least a year, the media has now turned on the company and claimed, just like Apple, it too is tracking users. A good (poor) example is this article by Declan MCCullagh at CNET.
The issue centres around Microsoft collecting GPS and cellphone tower ID data, and also MAC addresses to build up a map which can be used to find locations without a GPS fix. Microsoft does this by uploading anonymized information with a unique ID, but unlike the iPhone users are able to opt out. The Wall Street Journal has found that the iPhone collects tracking data even when location services are switched off.
Of course this ignored the real and original issue: the huge collection of data silently being accumulated on iPhones which can at any moment turn into testimony against a user, and just like when Jobs claimed other phones also had the antenna-gate issue, is simply an attempt to excuse Apple by painting others in the same brush.