Have you ever measured the ripple of your 3v3 supply under all load conditions? I see a small aluminum electrolytic cap where you should have a tantalum or an electrolytic selected for low ESR. Your supply could be loosing regulation or have very high ripple or worse, both.
Also, given that the LM2596 is a older design 3 amp regulator, L1 at 68uh might be too high of an inductance and you may well be operating below the minimum required load.
Your LM2596 pc layout has a very high impedance path in the ground connection (pin 3) by way of excessive thermal isolation provided. Those three tiny width traces to connecting the body to the ground plane are waaay too small.