Ferrite bead resonance
Yes, resonance of capacitance and ferrite beads can be a problem. They're pretty high Q inductors at low frequencies, which can come as an unpleasant surprise if there is something floating around to ring them up. 

You can try to improve things by increasing the capacitance to several uF so the series resistance adds damping or adding some parallel damping resistance, or a bigger ceramic cap + series resistor from VddPLL to ground. 

You have assumed the PLL Vdd acts as a high impedance, which may be pessimistic, but I suspect not totally unreasonable.