most usb flash disks have a real-time cache writing. so although it's advisable to safely remove them first, it shouldn't damage the flash disk nor your os. the trouble is, you can't tell which one's are which so whenever you just pull out a flash disk, you run the risk of corrupting files inside them (not so much your pc).
when it says it cannot be stopped, there may be a hidden process still running. this may or may not be a virus. but do a check on your flash disk and see if it corrects it.
when that happens to me, I turn off the computer then pull out the flash disk while the pc's off, specially when my data is too valuable to lose.