The most common problem caused by the bottom plates not being straight across or out of alignment is you just can't seem to get the door to fit tightly to the door stop. A common term for this is your door is out of plane. There are a few fixes to this problem, most of which is completed by trial and error.
Your door jambs (hinge and latch side) need to be in the same plane for it to close properly against the door stop. Let's say the door is out on the top latch side (sticking out on the top, beyond the jamb). To fix this you need to move the bottom of the opposite side (the hinge side) out in the same direction as the door is sticking out. This will push the top of the door inward. With the hinge side brackets attached, using a block of wood placed against the outside (the side opposite the hinges), slightly hammer the door in the proper direction. Close the door and check for fit to the stop.
You can also slightly move the top of the door in once you screw the latch side brackets to wall, by tapping slightly out
on the top of the jamb with a block and hammer. Sometimes you will need to move all 4 corners a little so everything fits snuggly. Normally not enough that it can't be covered with trim. You may need to ease the edge of the drywall so the trim will fit tight against the wall. Here is a trim video to view http://www.ezhangdoor.com/cutting-and-installing-door-trim
In other words, the door jamb gets installed plumb regardless of how the walls are. Usually you split the difference on all 4 corners of the door so that you don't end up having one part of the door jamb sticking out way past the drywall and one part of the door recessed way into the drywall. When your trim, the door casing, is applied to the opening it will cover up any irregularities.
Other problems may occur if the door is not installed plumb is that the door may want to continually swing open
(or closed) or it may even drag on the floor when opened wide. So you always try to hang doors plumb whenever possible.
The easiest way to visualize this would be to imagine your door and jamb lying flat on the flat on the floor. When all 4 corners are laying in the same plane or flat with each other, the door fits tight to the stop. If you raise any one of the corners off the floor, it will change how the door fits to the stop. So imagine needing to install your door in the opening so all 4 corners are in plane or flat with each other.