Flatpak's process ID namespace separation does not prevent a sandboxed app's kill(0, signal) or killpg(0, signal) calls from reaching processes outside the sandbox that share the same process group. A malicious or compromised Flatpak app can use this to cause denial of service by terminating processes outside its sandbox, such as the desktop shell.
Run Flatpak apps in a new session (setsid flatpak run ... or setsid() in the parent) or a new process group (setpgid (0, 0) in the parent), or avoid running untrusted Flatpak apps.