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When referring to previous document (manual, email, etc.) or a previous statement/reply I'm not sure of the difference between using 「点」, 「所」 and 「箇所」.
I would want to say something along the lines of:
「その点では、問題があります。」
「マニュアルには、一箇所は不一致になりました。」
「間違えたところは、４つあります。」
But to me, it seems as though 「点」, 「所」 and 「箇所」 are mainly interchangeable, granted the sentence might have to be slightly changed to accommodate the new word.
箇所{かしょ} (or 個所) is a physical "point" you can point where it is (that is, on the paper or elsewhere). You can translate it as "place", "spot" or "site". 点{てん}, by contrast, indicates abstract "point" you can only name in your mind (unless it means literal "dot"). Possible translations are "respect", "regard" or "aspect".
○ 論旨{ろんし}に筋{すじ}の通{とお}らない点がある。 There are illogicalities in the argument.
× 論旨に筋の通らない箇所がある。× 誤字{ごじ}を三点修正{しゅうせい}しました。
○ 誤字を三箇所修正しました。 I fixed three typos.
所{ところ} is a vague word more or less corresponds to "where". It could be used in place of both 箇所 and 点, just sounds more informal (colloquial) than them. Take care that 点 and 箇所 are counter words (as above), while 所 is not (× 誤字を一ところ修正しました。).
