Hi,
Firstly I had power-up sequence on my mind, but only fast pads may be driven high by this cause. Slow/Medium pads may only be driven low (see Table 20 in the device DS).
However as you can in the Table 1, some eMIOS pins has default state during and after reset with internal pull-ups enabled (other pull-downs or WKPCFG dependent).
If it is any issue or not is application dependent, if it could, user would have to use stronger external pull-ups (typically 4k7 or 1k) to overweight default internal weak pull resistor configuration or to use different eMIOS channels.