I wouldn't take any of them out, you can still hand turn the ones that are not turning on the disc. As long as they are turned at least 3 times per day they should be fine. I would also shoot a quick email off to Brinsea as CT said just to see what they say about it.
As some are turning and some are not I would think that is because the eggs are big. I've just had a read on Brinsea about the eggs sizes and disc available for the mini incubators and it says most duck eggs. Do you think your eggs are as big as a goose egg?