This is a warning for careless Steam users as my self that made this stupid mistake. If you do this Steam will for you you update a few files and there is no way that i could find to stop it. Well once this happens when STO launches and tries to patch it errors out. Luckily for you, I found out how to fix it by looking over the STO log files so if this happens to you here is what you do:
Make sure that the STO launcher is not running. (you can leave Steam running)
Go to C:\Program Files\Steam\steamapps\common\star trek online\Star Trek Online\Live\piggs
Rename 'bins.hogg' to 'bins.oldhogg'
Now Launch STO again from Steam and it should Patch as normal without generating a CrypticError().