You can use the Maintenance toolbar item or the Utilities toolbar item to verify the structure of the file system.
Warning: During the verification process, OnyX needs to temporarily lock the startup disk. The wait cursor (which looks like a colored pinwheel) will appear, and your computer will seem to be unresponsive. This is completely normal. This operation can take a long time to complete, so wait for the verification to finish.
It is possible to speed up the verification by deleting the Time Machine local snapshots beforehand.