Is this with Xwayland, or is Nautilus a native Wayland app?

Here's an example with the browser Epiphany: http://imgur.com/vwy6bF1.png
But this also happens with Xwayland- and other native programs.

Is this related to a specific toolkit?

E.g. if you open a context menu in weston-terminal's terminal area to pick, say, "Open Terminal", is that menu randomly positioned too?

Problems with Xwayland are a separate category from native Wayland apps, you should work in different bug reports on them. I recall Xwayland may have some problems in handling some window types, as X11 applications do not always tell what the parent window is, or something. You might want to check the existing Xwayland bug reports.

Let's track the native Wayland app problem in this report, shall we?

Thanks for your replay :)
Of course we can stick to native Wayland apps and I guess in case of Nautilus and Epiphany it's a GTK related bug.
I have to be more precise that not all context menus are affected by this bug.

Weston-terminal has the popup on the right position, where as for example Nautilus has some context menus on the wrong position.

Created attachment 108498 [details]
Epiphany GTK log wrong position of menus

Here is a log file from the browser Epiphany:
- Starting on line 11: Right clicking on a link. This context menu is on the correct position.
- Starting on line 18: Right click on tab. This context menu is displayed randomly. There are some GTK warnings/errors.
- Starting with line 22: Wrong position of main menu. No warning in log file :/

Yeah, please file this as a GTK+ bug in their Bugzilla.