No, you weren't doing it wrong.
(probably)
One of the first movement patterns I teach to a new athlete. Is the squat. Not surprisingly, when I start to work with a new lifter (even an experienced one), the first thing I want to assess is their squat pattern.
The reason for this is that there are 2 general squat patterns. One is not better than the other. It simply depends on what the purpose of the squat is and what the end goal is.
If the goal is to be a powerlifter, move a ton of weight, or do copious amounts of volume, the pattern will vary greatly from what we want to do to develop an Olympic lifter. One is not better than the other. And if you are looking to get good at the latter, and have been squatting as if you are trying to do the the former, all is not lost.
In the first scenario (regardless of high bar or low bar positioning) the lifter will initiate the movement by sliding the hips back, then squatting down. This loads the hips first, and leads to a more inclined torso position. As a result depth may be limited, but it is easy to load up a lot of weight like this. This style of squatting will tend to load the muscles of the posterior chain more (relative to the quads).
In the second scenario we 100% want a high bar placement. And the movement is initiated by the lowering with the knees going forward/hips going down. Relative to the previous style, the quads will be way more prevalent in moving the load. The torso will be upright and a greater depth will be able to be achieved. Due to all of this, the load moved will be a bit less.
And this is where people tend to get flummoxed: why would we want to squat with a pattern that will not allow maximal loading? Simply put because for an Oly lifter the squat is a means to an end, while for someone trying to squat a shit ton, the squat is the end goal.
For an Oly lifter we want to maintain as upright of a torso position as possible in the snatch, the clean and the front squat. Thus, it behooves us to get as strong as possible squatting with a vertical torso, even if that slightly limits the load. Another factor to consider is movement pattern. Our goal on a clean is to drop straight down. On the jerk our goal is to initiate the dip by keeping the hips from shooting back, so that they stay under the shoulders. If the squat pattern that we use develops the habit of the hips going back, you can sure bet that there will be some negative carryover to the technical lifts. I cannot count how many people I have worked with that have had a large connection between their back squat pattern and a seriously flawed jerk dip pattern.
That all said, for the most part, even if you have been back squatting in a more hip dominant pattern, all was not for naught. As long as you have the patience to work on mobility/mastering new positions and can accept that loads that used to be easy will be a challenge, the transition should not be too difficult. So no (as I have heard countless times) you have NOT been squatting wrong (unless your squat mimicked a good morning). You just need to adjust your squat to reflect your goals.