@john32123666 : Thanks for the info. In this case, it's qBittorrent rather than BitComet but it looks like it's the same issue (see https://github.com/qbittorrent/qBittorrent/issues/15964, for example).
From a Reddit thread on this (https://www.reddit.com/r/qBittorrent/comments/rguyp0/pad_files_being_created_how_do_i_stop_this/), it looks like there used to be an "Optimize Alignment" flag in qBittorrent that allowed you to turn that setting on or off. It doesn't look like that flag is still available, unfortunately.
I'm reluctant to switch to uTorrent, given its recent issues, advertising, and bloatware. I'll try the "V1" Torrent Format option instead of Hybrid to see if that solves both problems.
Thanks again for the help.