Why the pins of a port in some microcontrollers are not in order?
They are pretty much in order- counterclockwise increasing by bit number and separated by port number. 

They are organized by port (internally the data bus will be so organized, and the way you access the bits is similar) so you would not expect to find the LSB of one port next to the LSB of another. 

That said, there are various reasons why some microcontrollers might actually appear to have 'out of order' pins. One chip I am using right now has pins in bit order C5/C4/C3/C6/C7. It may be for backward compatibility or some other reason- the important thing is to pay attention to the datasheet.