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5/3/1 Squat Help

I’ve been doing the 5/3/1 program for about two months. I’ve seen great improvements in my bench, deadlift and push press. My squat was doing ok, but seems to be lagging behind, progress wise. Example, on the last set of my bench, it says to do at least 5, but do more if you can. I did 12 reps this week. Squat, I could only get 5. Could it be my assistance work? Please help. Thanks

It could be your assistance work, but no one will know unless you say what you are doing for assistance work. Also what are your numbers? How much weight did you start with? How much are you lifting now etc? Chances are your assistance work is fine. Progress comes in waves usually and with a program like 5-3-1 (if done properly with starting with less than your max) 2 months in is around when you should start getting to weight which is close to or heavier than what your original maxes are. Also you probably need to eat more.

Could be you just started heavier in the squat, try repeating a cycle with the same weight and aim to beat the reps.