I had been experiencing this recently too. My squat and bench weren't going up at all. My deadlift seems to go up no matter what I do, but that's a different story. I realized the problem: I wasn't benching or squatting.
I couldn't phathom why my bench had only gone from 285 to 300 in 5 months even though I had gained close to 10 lbs of muscle. I looked back and I had only actually included the bench press as part of a workout 4 times during those 5 months.
I had done every supplemental and accessory lift, but I wasn't benching. The same was true for the squat. I've made it a point to include the bench press and back squat every week for the next few training cycles and it should correct the problem.
If you haven't made the same mistake as me, then I would say that it just means you're at a point where you can really only focus on improving one lift at a time. The amount of work it takes to improve one lift means that you have to somewhat neglect the other two. We'll all be able to answer better when you post your workouts, however.