Using stock Android 6.0 (Marshmallow), the stock (LG V10) gallery application (version 4.72.6) is including pictures and other files that have a timestamp newer than the .nomedia file timestamp. I have not been able to test this on other devices to see if it is LG specific.
Recreating the .nomedia file will update the timestamp, and hide all older pictures. Also, the folder being index is a hidden one (starts with a '.'), not sure why it is also being indexed in the first place.
There seem to be a lot of topics on this indexing issue, but none associated with the timestamps. It appears this could have been done intentionally, but it is very undesirable since several applications cannot access the microSD card after the Android permissions update.