A job is sold from an estimate. It is performed against reality. It is billed from whichever of those two the person doing the billing had in front of them.
Most of the time those match closely enough that nobody looks. The times they do not are not evenly distributed, and they are not random.
The four places the gap opens
A part pulled from the truck and never logged. The job consumed it, the invoice never saw it, and the inventory count quietly disagrees with the shelf.
Labor that ran long for a real reason. The estimate said two hours, the job took four, and nobody wanted to have the conversation so the invoice said two.
A change made verbally in a driveway. The customer asked for something extra, the technician did it, and it exists nowhere in writing.
An agreement or warranty applied by habit rather than by terms. The discount was given because it usually is, not because this job qualified for it.
Why it does not show up in the numbers
Because the jobs still close and the invoices still get paid. Underbilling does not create a dispute. It creates a slightly smaller deposit than the one you earned, on a job you have already stopped thinking about.
Overbilling is the opposite problem with the same cause. It does create disputes, weeks later, when the margin is already booked and the customer is already annoyed.
The cheap version of the fix
Pick twenty closed jobs from last month at random. Not your biggest, not your worst, random. Put the work order and the invoice side by side and read them against each other.
Most owners who do this find something on more of the twenty than they expected. The exercise takes an afternoon once. The problem it finds happens every week.