First line of defence is frequent back ups. Even end user clients should make frequent backups. Even if the software is absolutely rock solid, the users aren't and sometimes you need to pull up a back up to correct user errors.
Next thing is to run a recover on the file and see if any issues are reported.
There are 3rd party tools such as FMDiff that you can purchase and use also to check the overall health of your file.
You may also want to examine the details of the relationships you have set up. If you enable the wrong delete options, you can get records disappearing from your file that you did not expect to have disappear when you deleted a record in a different table. These delete options are very useful, but must be used with care. They can form a mushrooming chain reaction where deleting a record in one table also deletes 100's or even 1000's of other records in any number of other tables.