I am generally not having an issue controlling my pets at all. I experienced one hole in the scenery the other day which swallowed them but other than that, no getting stuck or milling around.
I use Ninja and in combat if you just order your henchmen to attack a target without consideration of distance etc I notice that the neartest henchman will run and engage in melee sometimes throwing a midrange shuriken on the way. The other ones will hang back and shoot.
But if I take notice of what Im doing I can make my pets do just about anything. if you order to attack at long range, they will all use their bows and then one will run to melee and the rest will move to medium and....At medium range the Genin will use shuriken and then one will probably run in and melee. The Jounin uses his darts at range and at medium/close will usually throw caltrops and then melee. Sometimes I notice the jounin stops attacking after a smokebomb, I assume thats a bug like he loses his target or something.
So basically if I want them to melee and not stay at range I use goto and then once arrived order them to attack the mob, using the keypad controls from whichever genius wrote em its a simple matter to ensure all stay in melee.
My opening gambit on a single mob tends to be a volley of bow fire from all and then depending on if Im bothered about them all being in melee I 'goto' and reattack. I tend to throw a Darkest night on a mob in the group and then use defensive/passive to ensure the Ninja stay on everyone but the anchor mob.
In all honesty, I'm loving the tricksie nature of controlling the minions but I can make them do what I want in most situations. Im looking forward to see what I can do with the Oni when I get him in a few levels.