As per specification 27.272, Insert Subscriber Data procedure can be executed for multiple APN-AMBR modification. Multiple APN-Configuration AVPs can be included within the same "APN-Configuration-Profile" AVP.
After receiving the Insert Subscriber Data Request message, MME triggers Modify Bearer command message for each of modified APN configuration. In this particular case, MME should initiate two modify bearer command procedure, one for each modified APN-AMBR.
Please check the log at MME whether context-Identifier sent within the APN-Configuration is matched or not.
If valid context-identifiers are sent from HSS and MME is not initiating "modify bearer command" message even for both these valid context-identifier then this is considered as bug and need to be fixed.