There are built-in Geant4 commands for checking the generated geometry for errors.
First load slic in interactive mode.
slic -g ./mygeom.lcdd -n
Then execute the recursive geometry test, which will find overlapping volumes.
Idle>/geometry/test/recursive_test
This is generally the most useful test, though any of the commands in the /geometry/test directory are worth trying.
The command can also be put into a macro file and executed in batch mode.
slic -g ./mygeom.lcdd -m overlapCheck.mac &> overlapCheck.txt
After slic completes the recursive test, the file overlapCheck.txt will contain the full diagnostic output from the command.