Why do I have >10,000 cells in the 10X matrix produced by cellranger?
The raw data from cell ranger contains all of the barcodes detected in the experiment.  These raw barcodes are filtered by cell ranger to identify the barcodes that likely represent cells rather than empty droplets / dead cells. You can find the filtered data in the filtered feature-barcode matrices.  You can also examine the Run summary HTML file to see a summary of the cell ranger barcode filtering. 

The reason why there are so many raw barcodes is an important optimization by 10X to increase the cell capture rate compared to techniques such as drop-seq.  In a 10X experiment the number of gel beads is much higher than the number of cells which leads to a higher probability of a cell and a bead ending up in the same droplet.  This also leads to a large number of empty droplets with just a bead and some ambient RNA or a dead cell.  These all end up being sequenced and the empty drops tend to have a small number of unique molecules (the majority less than 10 UMIs / barcode).