When you are issued the piece of equipment, or toolkit, or whatever it may be, there will be an EIS (Equipment Issue Scale) which is a checklist of what is included. Any shortages upon issue should be recorded on a deviation record, along with the document numbers that the missing items are ordered on.
Sometime later, either at a routine check, an annual or special stocktaking, or return of the main piece of kit, the checklist is again referred to and shortages recorded.
Some items will be non-accountable, and some will be accountable. If the item is non-accountable, generally it just gets re-ordered. If it is accountable, then there may have to be a "loss of stock report". If the reason for the loss is rejected, you could be financially responsible.
Overages are generally just retained by the CQ or BQ, to be handed off to whomever is missing it. In the case of accountable items, they are theoretically brought on charge, although this is often not done.
During my years of service, the only time I saw guys have to pay for losses was when there was gross negligence.
Also, during a major stocktaking (ie: before a change of command), there are certain dollar amounts that are acceptable. If the dollar amounts are higher, then the level of write-off gets higher (ie to the CO, or even to the brigade commander) and there also may be a board of enquiry. BOIs are also held for losses of items that are mission essential and sensitive such as weapons. You do not want to be subject to a BOI.
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