Yes perfectly safe. There are advanced settings which I haven't messed with yet but if you just run it with the default settings its perfectly safe. I recommend running it about once a month to free up space and delete junk files. I know a bunch of people who use it aside from myself and none have had issues.
Your exact problem just came up yesterday in another thread. The solution is to remove the ios6 photos menu tweak and respring. Then run iCleaner and respring. Your problem should go away and your phone will be back to normal.
EDIT: Here's a link to yesterday's thread regarding this exact same issue. Seems like a common problem. Hopefully the dev resolves it soon.
https://forums.macrumors.com/showthread.php?p=15096090#post15096090