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I am fixing the wall, but it is creating a hole on the wall, I align it, but it messes the wall which does not look right. Not sure how to fix it, kinda confused if there is anyone who can help with this.
And if anyone can show me where to click, I am pretty visual about things.
That dialog box has an "Expand>>". Press it to drill down on what it is exactly that Revit is referring to. Perhaps disallowing join and/or joining (via Join Geometry) would resolve, but that condition shown in your screenshot looks pretty messy to me.
Pressing Unjoin Element resolve? Probably partially. Overlapping walls will remain.
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