Maybe it depends on the file you're reading? KOreader is usually more forgiving to the file format problems, unlike the built-in one.
One trick I noticed: if you want to use the built-in app, make sure to set your settings to shutdown the reader at least daily (e.g. after 8 hours of inactivity). Otherwise, it's getting more and more buggy and starting to crash.
KOreader doesn't have this problem.
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