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Okay, so this is because your fields are not strings; could you check the datatype of the fields prior to your formula tool? Perhaps they are set to bool? In which case your statement needs to look something like...
IF [2 Case EOQ?] THEN "Y" ELSEIF ![Days Cover Filter] THEN "Y" ELSEIF ![Case More Than £50?] THEN "Y" ELSE "N" ENDIF
With bool fields Alteryx will automatically check for a positive class hence [2 Case EOQ?] alone. If I want to check the negative class then I can add an exclamation mark in front.