I'm not very smart at this technical stuff (just a user, not a hacker), so it's probably such a basic thought that you have already determined that it is not your issue. But just to cover as many possibilities as possible...
Are you sure that you are taking possible buffering into account? IOW, there's a chance that you haven't actually copied "x%" of your data when it displays "x%."
Err... I'm probably not being clear. So: Your computer is a gasoline pump. Its buffer is a funnel. Your flash media (SD card, USB flash drive, .MP3 player, et cetera) is a lawn mower. You know that your mower will take ½-gallon (US, substitute your own measurement type here, or make one up - it's not important
), so you dispense ½-gallon of gasoline from the pump into the funnel. As you shut off the pump, you observe that the funnel still contains gasoline because the pump is capable of dispensing fuel far faster than the funnel can. You glance at the display on the pump and see that the operation is finished - but as most any absent-minded landscaper knows, if you do not take the fact that the funnel still contains gasoline into account, you will probably end up getting fuel in your boot.
Computers being smarter than the average funnel, lol, it's probably holding the progress status at 99% until the buffer is emptied so you don't end up... making a mess.
I was once transferring some files - don't remember what OS or even type (might not have been linux) - to a Corsair USB 2.0 Flash Voyager 8-gig thumb drive. I don't remember what its rated transfer speed is (I'm in my 40s, lol, and suffer from CRS Syndrome) but I do remember that, initially, the speed that was displayed in the pop-up activity box was vastly faster... But it soon settled down to ~the rated speed.
If I'm not mistaken, my current OS doesn't even display a transfer speed at first, but instead waits a short period of time. I assume this is to avoid displaying the speed of the transfer to the computer's buffer as opposed to the speed of the transfer from the buffer to the media.
The above is probably way longer than it needed to be and likely still doesn't make much sense.