What library are you using to create the windows? My guess is that your program is trying to set the window icon but fails, maybe because the file path is not valid.
If you call setIcon make sure the icon has been loaded correctly and has the correct format. The docs says it should be either 16x16 or 32x32 pixels. To test if this is where the problem is you could remove the call to setIcon and see if it shows the default icon instead.
It appears to be the fallback icon that is shown when there is nothing else to show. If you go to preferences -> appearance -> theme -> customize -> window border (something like that) you will probably see that some have this icon and some don't. I don't know if this is on purpose or if the default icon is simply missing from some window border themes.
Mint related, great point, this icon doesn't display using Ubuntu 16.04.
While trying to get into preferences -> appearance -> theme -> customize -> window border, I just observed this same icon on a Mint dialog window for 'Add/remove desktop themes'.
I can find no setting for window border, but this is a definite indication it is not related to Code::Blocks.
Addendum:
The fault icon does display only on windows not having their own icon located to the left of the title.
So I added an icon to my Code::Blocks test app wxFrame, that solved it.
My icon is displayed, not the fault icon.