To confirm, I ran into this too. I developed a first app at <app1name>.<pythonanywhere>.<com>. That is, I made my username the app name, since that seemed a more descriptive thing to share with others. Within that first app, I then developed a second app, piggybacking on the infrastructure of the first, until I eventually realized it warranted being separated off as its own thing. So then I upgraded to two apps, and it took me a while to realize that naming the second app <app2name>-<app1name>.<pythonanywhere>.<com> was ok but naming it <app1name>-<app2name>.<pythonanywhere>.<com> is not.
For context, the pressing need that made me figure this out was that I wanted both apps to have home pages without anything after ".com" (i.e. index() functions with path "/"). Now that I am following the <somestring>-<username> convention, it does work for both apps. The final step for me is now using two custom domains, where <customname1>.<customdomain> replaces <app1name>.<pythonanywhere>.<com> and <customname2>.<customdomain> replaces <app2name>-<app1name>.pythonanywhere.com. And it works great!