To draw an analogy, imagine your car runs out of gas near the top of a mountain. You put on the e-brake, and assess your situation. The nearest gas station is 20 miles away, and it's snowing, so there is no way you can walk it, and there is no other traffic on the road to offer you some help. Sucks to be you, but you should have planned better. You could let go of the e-brake, and roll down the mountain in reverse, but there is just a deserted valley at the bottom - it would not improve your situation. But, a ha! You realize that you are only 20' from the top of the hill. the gas station is still 20 miles away, but it's all down hill. If you can push your car to the top of the hill, you can then roll all the way to the gas station using gravity to power your car.
But, alas, a lawyer pops out of the woods, and hands you a document stating that you are not allowed to push your car up the hill and then use gravitational potential energy to get to the gas station, because Acme, Inc has been issued a patent on that process, and you are not allowed to use it without their consent. Coincidentally, you have an ongoing lawsuit against Acme, Inc, for a completely unrelated reason. They tell you "Drop this lawsuit, and we'll let you use our push-up-the-hill process to save your car".
That is pretty much what happened in this circumstance.
Yes, the engine failed to operate properly. No one is blaming the patents for that. The satellite got stuck in an unusable orbit due to the engine failure, but was otherwise still functional. Since launching things into orbit is very expensive, and the things being launched are very expensive, the company that owns the satellite will try pretty much anything within reason to recoup their costs. One option, popularized by Belbruno and Ridenoure from an similar incident in the past, involves using only a small amount of fuel, to send the satellite around the moon and back, which would make it possible to put the satellite into the correct orbit around the earth. THIS is what was denied them due to the patent on the low energy orbital transfer that Boeing apparently has. So, it is not the fault of the patent system that the rocket initially failed, but it is the fault of the patent system that the company was not legally allowed to recover it's still-functional property.
edit: I should add that, yes, SES Americom may have committed insurance fraud if they didn't disclose to their insurance company that the satellite was recoverable for $50M(the cost of dropping the lawsuit against Boeing). However, that doesn't change the fact that they were prevented from essentially running their engine at particular times due to patents.