There are many instances in the game where characters make opposed tests, and then something happens based on the degrees of success. The psychic power Blood Boil has the psyker make a Willpower test opposed to the target's Toughness test, and if the psyker wins the target takes 1 level of fatigue +1 per degree of success. So if the target fails his test by one and the psyker passes his by two, the target would be fatigued. My question is, when counting the degrees of success for this purpose, do you only count the two that the psyker got from passing his own test, or would it be counted as three because the psyker technically beat the target by three (2 - -1=2+1 for 3 degrees of success?) That seems to make sense to me, because the more the target fails, I feel the more he should get hurt. Or am I over-complicating this?

By the RAW, It would be 2, not three. But there are aspects of the opposed skill checks that I don't like, for example the fact that two failed rolls just reroll until someone succeeds. If there are two characters BOTH with little chance of success, that could be a lot of rolling.

The problem with counting the difference is that there are extremes of scale you will encounter when one side rolls low and the other rolls high. You could do it this way, as a house rule, only calculating the difference in degrees of success and failure. You could also limit the maximum degrees of success to the character's trait bonus. So if the Psyker has a WP bonus of 4, then even if the psyker gets 2 DoS, but the psyker's target failed by 5 more degrees, the extra damage would be limited to 4 as opposed to 7.