sample time required for variable frequency digital output of arduino mega 2560 microcontroller using simulink

Respected sir/madam I want to drive variable frequency from digital output of arduino mega 2560 microcontroller.At every digital output have different digital wave frequency. Like one digital output operates at 50 hz and400 hz from another digital output.and the sample time is 0.0001 But at CRO when i verified it is not coming,undesired frequency comes at output.where can be the problem.When i changed sample time 0.001 then another frequency i achieved at output??

[Rolfe Dlugy-Hegwer]

Hi Jiwanjot, Did it only have trouble with the higher frequencies?