Permissions are a "code" that is applied to any file that determines which users may access those files and what actions they may take on them. Generally, in UNIX, permissions are applied as a series of numbers from 0-7, so the OS knows what users are allowed to do. Simply, the possible permissions are:
0 - no permissions defined
1 - execute only
2 - write only
3 - write and execute (1+2)
4 - read only
5 - read and execute (4+1)
6 - read and write (4+2)
7 - read and write and execute (4+2+1)
These permissions can "go bad" for a variety of reasons. Applications change permissions when they are installed, when new files are created, when new users are created, etc. Also, because it's such a simple code that's appended to a file, it's easy for it to be corrupted or reset to 0.
Long story short - it's not something you need to worry about. If an application or file is acting strangely, try to repair your permissions - it might help. But most of all, don't worry too much because UNIX based operating systems do periodic checks all by themselves for invalid permissions, fragmented files, etc. It's built into the OS.