3 warnings appeared where VM start messages normally shows, about not able to show update icon and something about sys-usb.
As it is said in the title, where can I find the logs containing those messages?
I am not an expert, but try journalctl in dom0. It does show at least some messages like this for me.
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Two points:
If you’re looking to drive some process (if message X then, run process Y, feed to external log management etc.) based on these messages and are in fact seeking the actually log location; I think greping of journalctl (or something similar) as @fsflover has mentioned could be a sound approach. 
If you’d like to review “notifications”/warnings appearing in the systray/taskbar because they are not persistent long enough for you to view them, (depending on the window manager you’ve chosen to implement) you may/may not be able to find said information within “history” of the notifications applet found in the taskbar. 
Caveats:
A) The notifications applet may need to added to your systray/taskbar through window manager configuration
B) When many items are in the systray/taskbar, “unused icons” are often hidden to save space. Thus, you may find your notifications applet by finding+clicking something like “show hidden icons”.