Can't delete (some) photos, even not as root (Lollipop, XT1052)

Hi all,
I have a Motorola Moto X XT1052. Android 5.1, rooted, TWRP Custom Recovery, official OTA rom.
After the upgrade to 5.1, I recognized that I can't delete some photos. Strange thing is, this does not apply to all photos, some are deleteable, some are not. I use quickpic as gallery-app. If I select the photo and click delete, nothing happens. If I do so in the motorola gallery app, the photo seems to be deleted, but reappears after a reboot. I use the google camera app as well as the motorola camera app.

I opened a adb shell, navigated to /storage/emulated/legacy/DCIM/Camera and found a photo I can't delete. I became root and tried to delete the file via command line:
rm IMG_20150817_105806489_HDR.jpg, but the shell says "No such file or directory". If I then do
ll IMG_20150817_105806489_HDR.jpg, it lists the, file, so it's still there.

I then did
rm -f IMG_20150817_105806489_HDR.jpg and since I didn't get an error message, I thought it was fine, but
ll IMG_20150817_105806489_HDR.jpg still lists the file, so it's still there.

Anyone here has an idea?