Originally Posted by Jellby
That shouldn't cause the problem you are seeing, unless it doesn't remove the ligature table; i.e., if the font file is left with a table indicating that the combination "f + j" should use the glyph name "fj.lig", but the "fj.lig" glyph is undefined or blank. A good subsetting should either keep or remove both together, the table and the glyph (a better subsetting should keep both only if "f" and "j" are also included in the subset).
I know Calibre blanks out the characters not in use. I believe the table entry is still there as when the ligature is missing, and it's trying to be used, you get space instead of a character.