The total inability to unlock many achievements no matter what you do or try – or to even get Asobo to state clearly what will prevent unlocking of achievements and what will have no effect – would be near the top of the list of annoying bugs and flaws for me.
Second place would be the many annoying UI quirks such as windows that force scrolling but at the same time won’t resize to fit the available space and will just leave a huge blank area unused while forcing you to scroll inside the adjacent postage stamp-sized area.