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Any steps to repro this? I've tried manually triggering both of icons in both ways of appearing and it didn't happen.
Just reproduced this.
I had installed Xamarin.Mac 1.12 to be able to build MonoDevelop 5.9. Then I opened Xamarin Studio and selected Check for Updates on the stable channel. Xamarin Studio then started downloading Xamarin.Mac 220.127.116.112. The update icon was visible in the status bar. I then paused the download, opened an iOS project and added an unused variable and re-built the project to get a single warning icon to appear in the status bar. The warning icon shows next to the update icon but it looks fine there is a bar between them so they are spaced correctly. Now I went back into Check for Updates again and as soon as it starts to download Xamarin.Mac again I see the overlapped icons as in the screenshot.
This should be fixed by 935bdd81f1a8eca3de2e055c6d843306db68d2f as part of #33230
*** This bug has been marked as a duplicate of bug 33230 ***