Start with the squares.
Roofing is priced per square — one hundred square feet. The first number to check is the total squares on the estimate against the actual roof. A one-story ranch with a simple gable might be twenty-five squares. Add hips, valleys, dormers and a steeper pitch and the same footprint can be thirty or more. If the estimate was written from an aerial measurement and never verified on the roof, the squares are the first place it drifts.
Then the waste factor.
Shingles are cut around every edge, valley and penetration, and that cut material is waste. A simple gable might run ten percent; a cut-up hip roof with several valleys can run fifteen or more. An estimate that applies a flat ten percent to a complex roof is short before it starts. The waste factor should be stated, and it should match the roof you are looking at.
Look for what is written as one item.
Starter course, ridge cap, drip edge, ice and water shield, step flashing, pipe boots, ventilation. Each of these is its own material and its own labor. When they are missing, or absorbed into a single 'remove and replace shingles' line, the estimate is not wrong so much as incomplete — and incomplete is what a supplement is for.
Check the decking.
Decking is only visible once the shingles are off. A good estimate either includes an allowance per sheet with the expectation of a supplement once the roof is opened, or it explicitly notes that decking will be addressed on inspection. An estimate that says nothing about decking is assuming the deck is perfect.
Access and steepness.
Two-story access and steep pitch — generally over 7/12 — carry additional labor. These are legitimate, standard line items. If your roof is steep and the estimate has no steep charge, the labor is underpriced.
Code items.
Local code may require ice and water shield in valleys, drip edge at all eaves and rakes, or specific ventilation. If your policy includes code coverage, those items belong in the estimate under that coverage. If they are absent, ask why.
What to do with it.
You do not need to argue with the adjuster. You need a second estimate written by someone who has stood on the roof, with photos, that itemizes what the first one left out. That is the supplement. It is a normal part of the process, and carriers expect it.