You may not be aware of it, but Lr utilizes a database that is essentially always open when Lr is. The recommended practice is for that to be shut down when doing a backup either via Lr or via TM or whatever, since the open state of the db could result in a corrupted backup or problems when restoring. You might have been having the same issue when you cloned the database Aperture uses. Probably most of the time you can get away with either (indeed, many folks just use TM on Lr's catalogs and never have a problem). But it's not the safest method. Here, just as an example, is what CrashPlan says about it:
https://support.code42.com/CrashPlan/4/Backup/Backing_Up_Open_Files_And_Databases