One example is font and font size choices - because the system fonts and font rendering styles differ between platforms, it becomes very hard to tell what looks broken or 'not quite right' on the platform you're not used to. It's not uncommon to see sites launch with font choices that look rubbish on ClearType, but if you're not used to ClearType, it's hard to tell whether the rubbish is your fault or not.
Apple's excellent execution and Windows' (no-longer-deserved) poor reputation also mean you frequently hear excuses for this behavior like "Windows users won't care because they don't care about design" or "The Apple way is better, so we should do it that way on Windows too". Both of these are infuriating and lead to terribly designed products.