It's possible that this will happen if the following hold:
1) you install the BP Template Pack plugin using the auto-installer;
2) the plugin successfully copies the BP theme files to your theme;
3) your hosting space is configured in such a way that the Apache process is run by a different user than the one you use for FTP;
4) your hosting space is configured in such a way that files/directories created by the Apache user are given the permissions 644 or 755, ie they are only writable by the user.
This combination is not extremely common, because often if (3) and (4) are true, then (1) and (2) will fail (and vice versa). However, it's possible that you might have this configuration in your environment. If this is the case, you'll want to contact your system administrator so that new directories created by the Apache user are also writable by your FTP user.
I should note that this issue has *nothing to do* with the BP Template Pack. It just happens to arise in this situation because the BP Template Pack copies files around your server, which it then asks you to edit. This is uncommon among plugins. You'll probably find that if you try editing/deleting any other files through FTP that were created with WP's auto-installers, you'll see the same problem.
As for whether this involves "hijacking" your site, or otherwise make a "total mess" of things - I'm not sure I understand how this could be the case. BPTP copies *additional* files into your theme, but it does not edit any of your *existing* theme files. So the parts of your WP theme that have nothing to do with BP will continue to look exactly the same (from the markup point of view, at least) as before you installed BPTP. If you find that the BPTP styles are being loaded and you don't want them to load, just deactivate the plugin.