Okay, here was the situation:
With four starting characters, a Rogue Trader, a Seneschal, an Arch-Militant and a Navigator, the game began set in the Calixis Sector (Drusus Marches to be exact). The group received word of a smuggling ring that was ripe for the picking. They could take it down, or take it over. All they needed to do was get from Askephelion Secundus to the planet Fervious.
The journey started well; the ship entered the warp, the navigator found the Astronomicon's beam, the course was charted, and the ship sailed beautifully through the warp towards its target. Then came the time to exit the warp. Up till now the navigator had rolled very well, getting at least one degree of success on each of his rolls. But when he tried to exit, the poor guy rolled a 94. Being a beginner with Rogue Trader, I decided the ship had exited the warp, but was not near Fervious, but the next system in line, Monrass.
I ruled that the reason they had gone too far were two fold: a powerful warp engine (a Markov 1; capable of cutting down a journey through the warp by 1d5 weeks), and a warp storm that had appeared and dumped them farther than they expected. After a ill-recieved welcome from the governor of Monrass who wanted to be left alone, the group tried to go back the way they came, despite the warp storm warning. To keep it short, the group entered the warp, found a ghost ship as old as the Avengin Crusade, brought it out into real space, and ran away from the demonic entity that inhabited it.
My question to you: did I do anything wrong? If the Navigator fails one of his rolls, does it means he brings the ship off course, or do they spend a longer time in the warp than they intended? Should I make the dice rolls more lenient, since the Calixis sector is a well-traveled sector? What can be done to prevent Navigator mistakes in the future?
Also, is it possible to teleport onto another ship, even if both ships are traveling through the warp? And is it possible to have spaceship battles in the warp?