It doesn't make sense that you spent your time on that
You shouldn't have spent so much time on that
ご質問ありがとうございました。
「時間をかけるべき所の判断がおかしい」は直接訳しますと
「Your judgement of where to spend time is strange」になりますが、
「It doesn't make sense that you spent your time on that」で訳しました。
「それに時間をかけた意味分からない」みたいな雰囲気ですね。
「You shouldn't have spent so much time on that」は「それを時間をかけたのはよくない」みたいんですね。
「メインのCに使うべき時間を犠牲にするべきじゃない」は「You did not have to sacrifice the time you should have spent on the Main C」になります。
「ほぼ影響しないAやB」は「A and B didn't have such a big affect」です。
全部合わせて言いますと:
「You did not have to sacrifice the time you should have spent on the Main C. A and B didn't have such a big affect, so it doesn't make sense that you spent your time on that」になります。
役に立てば幸いです。