Duplicates of applications during restore?

[iOSfails]

I just flashed a ROM (aokp M4 for Gnex) and I created a titaniumbackup.zip for easier restoreation of apps and as I was restoring and installing I kept getting a message asking if I wanted replace the application with the same application. Almost like it backed up 2 of everything (luckily I only have 28 apps to restore)
What happened?

Only concerned because I don't want this to happen when I flash other ROMs in the future.

 

[cupfulloflol]

Did you give your market a chance to auto restore things?

 

[iOSfails]

No, but now I have an even bigger issue. I did a TiBu of my contacts and data, rebooted, and now I can't do anything! I get this pop-up "android.process.acore has stopped"
What happened?



UPDATE: No worries anymore. I did a factory reset and reflashed everything. Wipe dalvik too. Gonna restore contacts with Backup Assistant this time