It is not clear whether you are referring to your own internal audits or accreditation body assessments.
Any missing or noncompliant process or activity is a non-conformance (NC). Common examples are incomplete method validations or lack of recorded personnel competency. ISO 17025 does not require a classification as major or minor. The impact must be assessed by the responsible persons on a risk basis. Typically however, a Major NC would be a missing or deviant critical requirement, i.e. systemic problem (e.g. no Management review performed, ineffective or incomplete audit programme, or absence of critical environmental monitoring) whereas a Minor NC would be a missing activity, such as mandatory environmental monitoring record not completed for a day. If not evaluated and addressed minor NC could become a major risk.
For more information on ISO 17025 requirements, have a look at