While I mostly read ordinary fiction novels, not books with complex formatting and layout, formatting problems and rendering inconsistency are unfortunately quite common, yes. I generally do some simple edits to html and css so that formatting is more or less consistent in all the ebooks I read (no matter on which device I read them - I've read on Kindles and in Android apps in the past).
As to PDF, keep it away from me.
PDF is a very poor format for reading and so I avoid it whenever possible. Fortunately I have no need to deal with PDF files, all my reading is recreational.