Compacting SQLite databases while they are in use causes them to become corrupted. I've not checked if this is limited to SQLite but after compacting my system drive, all the programs I faced problems with had SQLite databases. These include Thunderbird, and Sticky Notes (From MS), among others.
Simply excluding .sqlite or .db files and their corresponding -shm and -wal files isn't enough, as programs such as Chrome use SQLite DB files without any extensions.