Wiring single circuit GFCI circuit breaker where a duplex GFCI breaker is shown in wiring diagram
You cannot combine neutrals from two GFCI breakers; it just won't work. A GFCI functions by comparing current flow between hot and neutral (for a 120 volt breaker) or hot 1 and hot 2 (for a 240 volt duplex breaker). Because you've combined the two neutrals, the current between the hot and neutral won't balance.
I have no information on modifying your spa, but if you cannot change it, you'll need a different panel and two duplex GFCI breakers.