There are a number of factors that could be responsible.....I can't really say without knowing you obviously....just off the top of my head...did you 'tweak' the program at all?? Were your strength gains in the same rep range? Meaning if you deadlifted 335x5 in the beginning and now you deadlift 365x5, it is NOT a strength gain to deadlift 335x5 in the beginning and deadlift 365x1 at the end, it is about workload and progressive overload, which is why sets/reps are constant.... ....Were you consistent or did you miss workouts and improvise?? Did you squat and squat correctly?....I mean full-range, free weight squats..Did you hit all your reps or did you require "spotting".......if you gained weight, you obviously were in caloric surplus, I am not what you'd call a proponent of sqeaky clean eating, but you DO have to eat enough of what you need, meaning some junk is ok in addition to nutritionally dense meals, as long as it is in addition to meals and not in place of them....you can't live off of hot dogs, beer, and Snickers Bars. How much stronger are you? Before and after numbers would be great, and typically what would you eat in a day.....don't post what you know you SHOULD eat like, post how you actually did eat typically.
These may sound like stupid, irrelevaant questions, but they are important.....a lot of times people aren't pleased with this because they used weights that were too heavy and missed reps and their spotter did some work (this eliminates the whole premise of the program, which is progressive overload).....some people decide to just start making up various rep ranges and swapping different core lifts in and out as they go......some people miss workouts and try to 'make it up'......some people fail to mention that they they took the 3 squat sessions and made 1 a Smith Machine half squat, the other a leg press, and the other a machine hack slide.....so, I am not saying you did all or any of this.....but since I don't know you, it is important to ask, because any of these would explain an aweful lot.