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The strong output drivers on this device require proper termination to maintain good signal integrity. This behavior has been observed with this part before, see this thread for some detailed suggestions: e2e.ti.com/.../1288287
Here are some things to check:
-Ensure proper termination and minimize output impedance discontinuities. It looks like their output termination is fine- I would also check the load impedance to make sure there isn't a mismatch that would require adding a series resistor (see section 8.1.2: 'Clock Outputs' of the datasheet on page 13)
-Ensure adequate power supply filtering, especially on the VDDO domains. They could try probing the VDDO pins to see if there is any voltage drop or fluctuation that corresponds with the ringing. The high frequency filtering caps should be placed physically near the VDDO pins. Based on the schematic they could also try adding a 10uF and 1uF filtering cap to each of the 2 VDDO rails. They might also try replacing the inductor with 0 ohm resistor (or small R value which does not introduce excessive voltage drop to the VDDO pin) to avoid possible increase in low/mid-frequency impedance and/or resonance between the ferrite bead and bypass caps.
-Follow good probing practices- it should be ok to use a differential probe as long as it is high impedance. Also, ensure that there is a short path to ground, as a long GND lead or grounding through a long trace increases inductance and can cause ringing to show up on measurements of high frequencies.