while your 90-days Non-Imm-O Family Visa is a done & dusted things, because you are married to a Thai husband, you son has no family connection to your husband. That's why he only can apply for a 90-days Non-Imm-O "dependent" Visa based on being the son of somebody on a Non-Imm-O Family Visa. Normally he could do the "change of visa type" from a tourist visa to the 90-days Non-Imm-O Dependent Visa on Immigration inside Thailand. However we are aware that some Immigrations won't touch the "change of visa type" process not even with a pair of tweezers. The Immigration who turned you down are one of these Immigrations because they are unsure which are the requirements. . . these are listed under Number 8 on this Immigration website .. . . . But please be aware that this Non-O Visa is limited to children only until the age of 20 . . . . . .
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Your problem is how to change your location and find an Immigration who is willing to accept it