pick and place cannot read LCC module
Yes, that is the cause of the problem (it expects a square pin at this location) .  I can think of two solutions.  1) you have to "tell" the program that it is OK to place a round pin at the mentioned position, or 2) "tell" it to ignore the shape of the pin going into the mentioned position.  

The 2nd solution is a bit more risky.  Try them both, and use 1 if both work.