When things start acting a bit weird, it's a good idea to completely shut the iPad off and restart. You should probably do this at least once a week (my unsupported opinion on frequency.)
Just hold down the power button for about three seconds. You'll get a power off slider. Go ahead and slide it off. Wait until the iPad completely shuts down and then restart it by holding down the power button for about three seconds again.
For more serious problems, when shutting it off doesn't work, you can do a soft reset. Hold down the power and home key for about 10 seconds, or until the Apple logo appears. Let go and wait for it to reboot. This will take a few minutes, so be patient.
If that doesn't work give us a few more details about the files, their size, and how you are working with them. Maybe someone will spot something. If the files are not sensitive you could supply a sample file here for others to experiment with.
