We assume that the method of measurement you specified in the contract required a bill item for rock trimming. In that case this is clearly an error in the bill of quantities that your project manager is required to correct under clause 60.6, and that correction will be a compensation event. To correct this, you will need to insert a new item in the bill of quantities for the trimming. This should be a rate if the work is not yet done, or a lump sum price if it is already done (see the 2nd and 3rd bullets of clause 63.13), although you can agree with the contractor to do it any other way if you wish.
The rate or lump sum price you will need to use must reflect the defined cost to carry out the work involved in the new bill item (see clause 63.1). In addition, you must assume that your contractor did not allow for this in its programme (see clause 60.7). If this work delayed planned completion, then the completion date will need to be changed as per clause 63.3. In addition, the defined cost for any delay will need to be included in the rate or lump sum price.
Clause 60.5 (and 60.4) is irrelevant. You did not have any quantity for this work in the bill of quantities because there was no item stated in the bill of quantities for it. Therefore clause 60.5 does not arise. It only arises if you have something in the bill of quantities for an item of work, but the quantities involved were very low when compared with the quantities actually required. The delay element is picked up anyway in the valuation of a compensation event under clause 60.6, as it would be for any compensation event, as explained in the previous paragraph.