Werner.....It can lead to problems becasue if Oscillation exists just at the time the microcontroller software sampling routine is trying to read the two input signals the pulse stable time may fail the setup time to the input of the register. Under these conditions the microcontroller input may be metastable and the software can read the opposite state than the hardware is in. This can lead to your state machine getting out of step with the encoder. This can even exist in the cases where the microcontroller design synchronizes the inputs by the pin before presenting the output of the flipflop to the port read instruction.

The HP / Agilent chip uses a series of
synchronizer flip flops in series in its design that virtually (but not 100.00000000%) eliminates the metastable problem.

Michael Karas