Odd rotation on a pipe

Not sure what you're doing - it works for me...

Create a new Scene and drop this on the Main Camera:

 using UnityEngine;
 using System.Collections;
 
 public class PipeRotation : MonoBehaviour {
 
     GameObject[] pipes = new GameObject[3];
     GameObject selector;
     int sel = 1;
     bool animating = false;
     void Start () {
         Camera.main.gameObject.AddComponent<Light>().range = 30;
         pipes[0] = Cyl(0,-3.5f,0, 0,0,0, 3,0.1f,3);
         pipes[1] = Cyl(0,-3.5f,0, 0,0,0, 3,0.1f,3);
         pipes[2] = Cyl(0,-3.5f,0, 0,0,0, 3,0.1f,3);
         Cyl(0,-3,0, 90,0,0, 1,1.5f,1).transform.parent = pipes[0].transform;
 
         Cyl(0,-3,0, 90,90,0, 1,1.5f,1).transform.parent = pipes[1].transform;
         Cyl(0,-3,-0.75f, 90,0,0, 1,0.75f,1).transform.parent = pipes[1].transform;
 
         Cyl(0.75f,-3,0, 90,90,0, 1,0.75f,1).transform.parent = pipes[2].transform;
         Cyl(0,-3,-0.75f, 90,0,0, 1,0.75f,1).transform.parent = pipes[2].transform;
         Cyl(0,-3,0, 0,0,0, 1,0.5f,1).transform.parent = pipes[2].transform;
         
         pipes[0].transform.position += Vector3.left*4;
         pipes[2].transform.position += Vector3.right*4;
 
         selector = Cyl(0,-3.5f,0, 0,0,0, 3.5f,0.05f,3.5f);
     }
 
     GameObject Cyl(float x, float y, float z,
                    float rx, float ry, float rz,
                    float sx, float sy, float sz) {
         GameObject o = GameObject.CreatePrimitive(PrimitiveType.Cylinder);
         o.transform.position = new Vector3(x, y, z);
         o.transform.rotation = Quaternion.Euler(rx, ry, rz);
         o.transform.localScale = new Vector3(sx, sy, sz);
         return o;
     }
     
     void Update () {
         float osc = 0.5f * Mathf.Sin(10*Time.time);
         selector.transform.localScale = new Vector3(3.5f+osc,0.05f,3.5f+osc);
         if (!animating)
         {
             float horiz = Input.GetAxisRaw("Horizontal");
             if (Mathf.Abs(horiz)>0.5f)
             {
                 sel = (sel + 3 + (int)Mathf.Sign(horiz)) % 3;
                 StartCoroutine(MoveSelector());
             }
             float vert = Input.GetAxisRaw("Vertical");
             if (Mathf.Abs(vert)>0.5f)
             {
                 StartCoroutine(RotatePipe(Mathf.Sign(vert)));
             }
         }
     }
 
     IEnumerator MoveSelector() {
         animating = true;
         Vector3 target = new Vector3(sel*4-4,-3.5f,0);
         while(selector.transform.position != target)
         {
             selector.transform.position = Vector3.MoveTowards(selector.transform.position, target, 0.3f);
             yield return null;
         }
         animating = false;
     }
 
     IEnumerator RotatePipe(float direction) {
         animating = true;
         GameObject pipe = pipes[sel];
         Quaternion target = pipe.transform.rotation * Quaternion.Euler(0,direction*90,0);
         while(pipe.transform.rotation != target)
         {
             pipe.transform.rotation = Quaternion.RotateTowards(pipe.transform.rotation, target, 3f);
             yield return null;
         }
         animating = false;
     }
     
 }