Hi Ugue,
You need to specify the axes where you want to plot the figure. Right now, since you have not specified any axes to plot to, it plots to the "current axes" and current axes in your case is "axes3". Hence it plots both accelerometer data and GPS data in same plot. To rectify this, you can specify the axes that you want to plot to in the "scatter" function and in plot_google_map function.
The axes can be specified by making use of "handles" structure in the GUI. I have attached an example in which I am using following syntax to plot to a specific axes:
scatter(handles.axes1, sin(0:0.1:2*pi),cos(0:0.1:2*pi)); %To plot to axes1
plot(handles.axes2, cos(0:0.1:2*pi)); % To plot to axes2
I hope this answers your question.
Regards,
Vaibhav