An other way you can force those problems is with automatic import via folder and a wrong setting how to generate metadata with mass imports. In case you set up metadata read by book content rather than file name and in addition a not so good setup for adding books, you sometimes can come in trouble if metadata are not available or scrap (saw this mostly in combination with PDF formats). If I use this way, I often change the behavior to generate a title from the file name as these are more likely unique (in my use cases) and better in handling especially with automated unsupervised background tasks.
As was mentioned, a bit regular housekeeping is always a very good idea to keep everything smooth with no surprises.
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