I recently bought the game after editing picture files for Japanese American Football leagues and some for fictional and other Japanese sports teams. The 1st sim league I tried was the 66 teams so I could fit most of the X-League and JPFF teams. I'm having a recurring issue each season where a error message says the team edited in place of the Louisville Greenjackets had too many players starting the 1st 2 seasons and then in the 3rd and after they have too few. And I checked the free agency period and multiple are not signing anyone and even when I use the auto fill roster they only reach 44/53. It turns out it's multiple teams not signing and the only fix seems to be manual control of 66 teams.

May need to adjust practice squad counts, roster minimums and maximums, and possibly the salary cap depending on your situation. Hard to tell from this post whether they're not signing due to lack of funds, or lack of players in free agency at required positions.