It does not mean that...; it's not that... — a colloquial expression used to deny or to soften a conclusion.
彼のことが嫌いなわけじゃないが、今は距離を置きたい。
It's not that I dislike him, but I want to keep my distance for now.
お金がないわけじゃないが、旅行には行けない。
It's not that I don't have money, but I can't go on the trip.
それが原因だというわけじゃないと思うよ。
I don't think that necessarily means it's the cause.