So, why the hell would two Imperial Forces fight each other? Well luckily, the last time I checked, the 40k Universe is full of paranoia, back-stabbing and other unpleasant motivations. Not all is rosy in the Imperium of Man.
Before we begin, it helps to have an established story for your force. Are they an expeditionary force? Are they defending their homeworld? Are they on campaign? If you have a foundation, it's far easier to build a solid house on top of it.
Here are some ideas:
1. It's a wargame. Real armies do these all the time. To prepare for war, one plays at war. This is probably easiest to rationalize, though it's kinda weaksauce for the creative types.
2. Rivals come to blows. There's a Forbidden Item of Great Power on the planet below, and both side are arguing about how to dispose of it. There is no compromise, there is no backing down, and it must be settled by blood.
3. A Radical (Heretical?) Inquisitor has manipulated one or both of the forces. Which would be a neat backstory for a branching campaign, if one your other friends has a large Daemon Hunter force, you can have the two forces join against the manipulating bastard at the end to put him down.
4. Your Chapter is skirting the razor's edge of heresy, loyal until that last straw breaks the camel's back, then the descent into howling madness begins!
Here we have a pre-battle story illustrating #2
"It seems the Sisters have not forgotten Armageddon, Brother-Sergeant. They hound us at every step."
"They seem to know our objective, Brother Chaplain. Their agents must be very well informed. Not that their information will help them. If they but knew our true cause, they would likely join us." Brother Sergeant Lucius's auto-senses tracked the heat-bloom coming off of the sister's lead Immolater. The rest of the Sisters milled about in the pre-dawn gloom, taking positions covering the impact crater.
It had been several years since Chaplain Odio found the tome that led them on the quest to recover the mortal artifacts of Angaron. If the Liber di Furia Inumana could be believed, then the gathered items they found could banish Angaron into the Immaterium forever.
"I doubt that highly, Lucius. The Ecclesiarchs are a prickly lot. If they are even aware of our quest, I doubt it would matter. They see us as tainted, no matter what." He sighed as he watched the Sisters take the high ground far in the distance. "It is time we teach them a lesson. Release the Annointed Ones from their chains. They could do with a hunt."
Odio tightend his grip on his Crozius, it's spiked head arcing with energy in response to the sudden rage that gripped him. Odio turned to the Fourth Company, his Brothers in Arms.
"Once more, we are opposed by those that would keep us from our quest. Once more, we must fight and spill blood for what we know to be true. The skull of the last victim of Angaron as a mortal man awaits us in that crater. The Skull Last Taken will be ours, Brothers! We attack at dawn! None shall stand against us! BLOOD IN HIS NAME!"
"BLOOD IN HIS NAME!"
As one, the Flesh Tearers advanced....