I persistantly save my team in a custom formation, never had a problem. What I have found does cause this issue, though, is when you save with a custom formation that is somewhat unusual in the amount of players in each 'sector'. For example last year I wanted to experiment with a 4-1-5 formation (don't laugh :p). I kept getting the 'no spaces left for this position' or whatever it is error when trying to move my players in the desired places, upon reloading, bam, same error as above.