i wouldn't say its a design "flaw". that implies its a mistake.
it's just an inherent downside. without injectors in the intake ports, there's nothing there washing away carbon deposits anymore. you cant fix it unless you move the injectors back to the ports and give up the benefits of DI. the "fix" is to run a catch can, and preferably not run the line back into the intake at all. but manufacturers have their hands tied here. for emissions reasons they cannot just dump the exit to atmosphere, and for cost reasons they wont implement an effective catch can system.
Toyobaru got it right with the FRS/BRZ. it has both DI and port (total of 8) injectors.