Yes, that happens. It's been mentioned in the quite numerous battery threads around here repeatedly.
- You may have one or more corrupt files. Hook the card up to a computer (via a cardreader or slot) and do a global search for 0kb files on it. Delete all 0kb media files (ignore the playlists and .nomedia.)
- Drop a .nomedia file in every folder you don't need to see in your gallery, Stock video or Stock musicplayer. This tells mediascanner to skip that folder. It applies to all subfolders as well, so dropping one in your ebook folder is enough to exclude all folders within that folder. (so anything containing stored maps, documents, textfiles, apks, appfiles (you can safely srop one in the Android folder, if Android hasn't already done so.), books, etc canbe safely excluded. If you find you need the folder shown somewhere after all, just delete the file.)
You can copy the ones already existing in several folders on the phone (Android creates them.). May need to enable hidden files first.
For instance, I have one folder containing a total of 24.238 files in 1.439 folders. These are all saved websites for documentation when I don't have internet access. Before I dropped a .nomedia file in my 'Websites' folder, my battery drained within a mere few hours, and the phone always ran hot. Dropped a .nomedia file in there, problem solved. Indexingservice skips the folder entirely, and I can access it via the filemanager (ES in my case, but stock works too.)
The Stock players rely on the Indexingservice. If you use an alternative music player, you can also add one to your music library. (Keep in mind this might disable the album arts. On N7 it works fine, haven't tested the rest.) Quickpic can be set to show folders hidden by a .nomedia file.
Videoplayers use Indexingservice, so adding a .nomedia file to the video folders excludes them from the videoplayers. You can still launch the video from your filemanager though. No issue there.
Oh, and ringtones, alarms and notifications require indexingservice, so don't add a nomedia file there.