Yes, the breakdown of the lines will happen if you or the AI targets individual units. What happens is that if the targeted unit turns or moves, the "lead computing" is done to plot an intercept course. This makes a mess of the lines since both the human and the AI end up with a bunch of odd vectors.

As humans we are learning to overcome this problem. With phalanx units I order my entire battle line to "march through" the enemy battle line. I do the same with some other infantry. When contact is made I take control of individual units to redress the line or halt/turn/flank/etc. as needed. CA needs to program the AI to do this as well. Presently the AI battle line is prone to disintegration. However, it does a somewhat better job of meeting mine if I do the "march through" because the lead computing is nice and symmetrical.

There are some problems with group marching that can cause faster units such as cav, etc. to advance in front of the heavy infantry, even if they were grouped behind (another area CA needs to address.) I think this is causing a portion of the suicide daimyo behaviour. Still the AI should not be charging the general forward in the first place.