The batch is inconsistent
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The syrup kept changing while you packed
Syrup held hot during a long fill keeps evaporating, so the last bottles are denser than the first and darker as well. Measuring at the start of a run and not again is how a batch leaves the building spanning most of the legal window.
The raw material moved
Sap and juice change across a season, and the same process applied to later material gives a different color and flavor. That is natural and it is only a problem if the label implies otherwise, which is a reason to record what went in alongside what came out.
Two batches got blended without a record
Combining a thin batch and a thick one to land in the middle is a legitimate practice and it has to be recorded, because the result is a new batch with its own code and its own reading. Blended stock with no record is stock you cannot trace when a complaint arrives.
The fix is measurement, not more care
Measure at the start and end of a run, record both, and treat a wide spread as a signal that the run was too long or the holding temperature too high. Care without measurement produces a maker who is confident the batch was consistent and cannot show it.
Check whether it is really one batch
Before diagnosing anything, confirm the bottles in question came from one run. Stock from two days packed into the same cases, or a blend that was never recorded as its own batch, produces exactly this symptom and has nothing to do with the process. The batch code is what settles it, which is the argument for coding every bottle rather than every case.