There are multiple things that could potentially cause corrupted files, however they are not generally the result of any actual code bugs. Here's the first thing to try:
Please delete the affected files and then run a force-verify in the launcher. You can get to this in the launcher, under Options. Once that has run, the corrupted files should hopefully be fixed.
If that alone does not fix the issue, please submit a Tech Support ticket at
http://www.startrekonline.com/support/tech and post in the PC & Technical Issues forum for assistance troubleshooting. Corrupted files can be caused by a number of different kinds of hardware errors as well, and they can help run you through necessary fixes and workarounds, and potentially pinpoint what is causing the issue.
Hope this helps!