HTML formatting issues CAN cause this, so YES it can be caused by 'software'.
I have had this happen repeatably only on one book.
I noticed that it only occurred at one or two spots in the book, and changing the font size to change the 'pagination' of the book would keep it from happening even in those spots.
The book that was doing this in my case was a free title from the Internet, and unfortunately, you can't control the quality of these free titles, so if this is only happening on a few titles or on books from a particular source, then I wouldn't worry about it.
Fortunately you don't run into it often. For example, I have over 1200 titles that I downloaded from the public domain section of
www.feedbooks.com and I haven't had a single problem with any of them.
If it's a book you care about, you could try running the book through a format conversion in Calibre, from HTML to LRF or MOBI and back to EPUB to see if that fixes it.