Is it right to say about something inefficient, for example: 'This process is poorly organized. It's like one leg is running and another is walking?'
That phrase is not a common idiom in English. However, a similar idiom related to limbs exists and means something very similar:
the left hand doesn't know what the right hand is doing
The idiom is defined per Dictionary.com:
The actions are uncoordinated, especially when they are contrary, as in
Purchasing has placed the order and accounting says we can't pay for more supplies this month; the left hand doesn't know what the right hand is doing.
It relates to the phrase you described above in that it makes a figurative description of inefficiency by pitting the one arm against the other, similar to "one leg is running and another is walking."