An AFE is an estimate of the expenditure for a particular well or project that has received the requisite approvals at that stage under the relevant agreement and internal process. It sets out the planned work and expected costs so the operator and others can assess the proposed expenditure before work begins. The AFE amount is a budget and not a record of the actual cost of the work.
An incurred cost is one which relates to work done or goods received (regardless of whether it's ultimately recorded as an expense or a capital cost). The actual amount will of course vary from the AFE as the invoices come in and the costs get coded to the project. A JIB invoice is a completely different proposition. It's an invoice to a partner for its share of the chargeable costs under the relevant agreement. A $1m AFE in no way implies that the operator has spent $1m or that a partner owes $1m.
The governing agreement will specify who has to approve the AFE and when the operator is required to seek a revision, a supplemental authorization or a partner notification. In the case of a jointly operated well, this will be the Joint Operating Agreement. You'll need to refer to the relevant agreement and the approved AFE prior to treating a variance as an authorization issue. There is no one dollar or one percentage threshold that applies to all projects.