If you've pasted more than one cell, that code would be problematic. You need to add the ability for the code to "loop" through all the multiple pasted cells that intersect your watch range, like so:

Dim cell As Range, wsSheet As Worksheet

If Not Intersect(Target, Range("$A$1:$O$100")) Is Nothing Then
    For Each cell In Intersect(Target, Range("$A$1:$O$100"))
        Sheets("Alt_Runsheet").Rows(CStr(cell.Row) & ":" & CStr(cell.Row)).EntireRow.Hidden = UCase(cell.Value) = "NO"
        Sheets("Runsheet").Rows(CStr(cell.Row) & ":" & CStr(cell.Row)).EntireRow.Hidden = UCase(cell.Value) = "NO"
        Sheets("Breakouts").Rows(CStr(cell.Row) & ":" & CStr(cell.Row)).EntireRow.Hidden = UCase(cell.Value) = "NO"
    Next cell
Else