Sub MoveData()
    Sheets("Grain2").Cells.ClearContents
    Sheets("Hop2").Cells.ClearContents
     
    DestnColumn = 1
    For Each are In Sheets("Recipe").Columns(1).SpecialCells(xlCellTypeConstants, 2).Areas
         'are.Select
        GrainDestnRow = 1: HopDestnRow = 1
        For Each cll In are.Columns(1).Cells'deals with he merged cells (try not to use merged cells with VBA - they're very hard work!)
             'cll.Select
            CurrentItem = Application.Trim(cll.Value)
            Set GrainFound = Sheets("Inputs").Columns(1).Find(what:=CurrentItem, lookat:=xlWhole, LookIn:=xlFormulas, searchformat:=False)
            If Not GrainFound Is Nothing Then
                Sheets("Grain2").Cells(GrainDestnRow, DestnColumn) = CurrentItem
                GrainDestnRow = GrainDestnRow + 1
            End If
            Set HopsFound = Sheets("Inputs").Columns(3).Find(what:=CurrentItem, lookat:=xlWhole, LookIn:=xlFormulas, searchformat:=False)
            If Not HopsFound Is Nothing Then
                Sheets("Hop2").Cells(HopDestnRow, DestnColumn) = CurrentItem
                HopDestnRow = HopDestnRow + 1
            End If
        Next cll
        DestnColumn = DestnColumn + 1
    Next are
End Sub
Problems:
Merged columns A and B in Recipe sheet
Several syntax errors (Recipe instead of Sheets)
Names of variables not consistent.

For this last, I should have included some Dim statements at the top of the sub's code as well as a single Option Explicit line at the top of the code module:
Dim DestnColumn, are, GrainDestnRow, HopDestnRow, cll, CurrentItem, GrainFound, HopsFound
and this would have shown up spelling differences.