Hello erik.ziel@autoliv.com,
With our toolbox we provide a great example called ftm_qd_s32k14x. This example shows how the QD works either in Count and Direction or Phase A and Phase B mode on the S32K144EVB. You need to use the FreeMaster and to connect the pins like in the model description.
However, the best explanation about the QD module, can be read from the S32K-Reference manual.
Long story short:
Quadrature Decoder – Count and Direction Encoding mode
In this mode, the phase B input value indicates the counting direction, and the phase A input defines the counting rate. The FTM counter is updated when there is a rising edge at phase A input signal.

Quadrature Decoder – Phase A and Phase B Encoding Mode
In this mode, the relationship between phase A and B signals indicates the counting direction, and phase A and B signals define the counting rate. The FTM counter is updated when there is an edge either at the phase A or phase B signals.

If you want to use the Count and direction Encoding Mode please also select this in the QD Mask, because in your example it looks like there is a bad setting.
Hope this helps you,
Marius