Read MoreUber's PR missteps aren't hurting business ... yet
Uber says use of its data is allowed only for a limited set of legitimate business purposes." But now there are questions about how airtight that policy really is, and what "legitimate business purposes" really mean.
Ellen Cushing, an editor at San Francisco magazine, says that several Uber employees warned her that Uber executives might look into her travel logs.
Buzzfeed News reported that an Uber executive in New York allegedly tracked one if its reporters without her permission.
"We have not, do not and will not investigate journalists," an Uber spokesperson told CNBC.
Would it be illegal to track users without their knowledge?
That depends, says Gautam Hans of the Center for Democracy & Technology. He says Uber could be in trouble if it uses data for reasons outside of very specific business purposes.
"We understand that Uber needs to know where we are," Hans said. "But the hope is that the company uses that information appropriately."
Read More Uber and the media debate
The FTC and the California attorney general's office did not immediately respond to CNBC requests for comment.