My HFS+ startup disk is case-insensitive like most people’s (because Adobe still can’t get their s**t together and write the paths to their installed libraries in the correct case) and I’ve noticed that changing the casing of a file name makes Alfred index the file twice.
This, presumably, is because the old entry is checked first and since the filesystem is case-insensitive, the system reports that, indeed, the file still exists. Later it is added to alfred’s database with the new casing and because the database index (or the function that checks for duplicates) does not consider these two entries the same, it will add a new entry for the new casing.