yea, i would consider mailing a box of dog shit to whomever installed that system.
if this was my yard, the very least i would do is either shut off the shaded shrub popups, im going to go out on a limb and say they will probably be ok if the shrub is established.
if this is not an option, i would reduce the flow rate on the shaded popups as much as possible (some will not allow for this).
no amount of software can accommodate poor irrigation design. sorry bro, maybe the wizzard @emil has something up his sleeve.