Some forms will get put in the forms box even if they should not

One blatant example is with the LA box. Selecting sorting Forms after Species will put the three final stage starter in the first Forms box (in this case Box 9).

Another one I found is in the LZA box, same settings as above will put Vivillon in the Forms box, leaving missing Vivillon in the species form, so going from Spewpa to Weedle