For some reason, evnt.Axes in your toolbar button callback is not equal to the corresponding axes that you store within app.myaxes. I'm a little confused, but I think it might be related to the following, which you can run yourself at the command window:
>> ax = uiaxes;
>> isequal(ax, ax.Toolbar.Parent)
ans =
logical
0
and
>> class(ax)
ans =
'matlab.ui.control.UIAxes'
>> class(ax.Toolbar.Parent)
ans =
'matlab.graphics.axis.Axes'
The documentation for UIAxes says you can use axtoolbar on UIAxes objects, but when you do so, the parent of the new toolbar is set equal to the parent of the previous toolbar, which as shown above is clearly not the UIAxes in question. Maybe it is a bug that the UIAxes' toolbar's Parent property seems to refer to a regular old Axes, or maybe I am just misunderstanding something.
At any rate, you can solve your issue by passing in the specific axes to your toolbar button callback instead of using the axes stored in evnt.Axes:
btn.ButtonPushedFcn = {@(~,~,ax) (delete(ax)), ax}; % Click on this tool to delete axis
(edit) Just to show that the above is only true for UIAxes:
>> ax = axes;
>> isequal(ax, ax.Toolbar.Parent)
ans =
logical
1
(edit #2) Above was done in R2019a.
